Methods and compositions for determining resistance to androgen receptor therapy

ABSTRACT

Described herein are modified androgen receptor polypeptides that are resistant to inhibition by an androgen receptor inhibitor. Described herein are compositions, combinations, and kits containing the modified androgen receptor polypeptides and methods of using the modified androgen receptor polypeptides. Also described herein are methods of using the modified androgen receptor polypeptides as screening agents for the identification and design of third-generation androgen receptor modulators. Also described herein are third-generation androgen receptor modulators that inhibit the activity of the modified androgen receptor polypeptides. Also described are pharmaceutical compositions and medicaments that include the compounds described herein, as well as methods of using such androgen receptor modulators, alone and in combination with other compounds, for treating diseases or conditions, including cancers, such as castration resistant prostate cancers, that are mediated or dependent upon androgen receptors.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional application to U.S. patent applicationSer. No. 14/417,515, filed Jan. 26, 2015, which is a national stageapplication of Patent Application No. PCT/US2013/052395, filed Jul. 26,2013, which claims the benefit of U.S. Provisional Application Nos.61/676,842, filed Jul. 27, 2012, 61/783,763, filed on Mar. 14, 2013 and61/829,123, filed on May 30, 2013, each of which is incorporated hereinby reference in its entirety.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING SUBMITTED AS A TEXT FILEVIA EFS-WEB

The instant application contains a Sequence Listing, which has beensubmitted as a computer readable text file in ASCII format via EFS-Weband is hereby incorporated in its entirety by reference herein. The textfile, created date of Feb. 27, 2017, is named 103693_000574_SL.txt andis 136.663 bytes in size.

BACKGROUND OF THE INVENTION

The androgen receptor (“AR”) is a ligand-activated transcriptionalregulatory protein that mediates induction of a variety of biologicaleffects through its interaction with endogenous androgens. Endogenousandrogens include steroids such as testosterone and dihydrotestosterone.Testosterone is converted to dihydrotestosterone by the enzyme 5alpha-reductase in many tissues.

The actions of androgens with androgen receptors have been implicated ina number of diseases or conditions, such as androgen dependent cancers,virilization in women, and acne, among others. Compounds that diminishthe effects of androgen signaling via the androgen receptor and/or lowerthe concentrations of androgen receptors find use in the treatment ofdiseases or conditions in which androgen receptors play a role.

SUMMARY OF THE INVENTION

Described herein is the identification of modifications in the androgenreceptor (AR) that confer resistance of patients to treatment with afirst- or second-generation androgen receptor antagonist. In someembodiments, the modification is a substitution of phenylalanine atposition 876 of an AR polypeptide. In some embodiments, the modificationis F876L. In some embodiments, the modified AR polypeptide is resistantto inhibition by a second-generation androgen receptor antagonist isselected from among ARN-509, enzalutamide (MDV3100), and RD162. In someembodiments, the modified AR polypeptide is resistant to inhibition by afirst-generation androgen receptor antagonist selected from amongbicalutamide, flutamide, hydroxyflutamide or nilutamide. In someembodiments, the patient has a cancer. In some embodiments, the canceris a prostate cancer, breast cancer, liver (i.e. hepatocellular) cancer,or bladder cancer. In some embodiments, the cancer is acastration-resistant prostate cancer. In some embodiments, the modifiedAR polypeptide exhibits one or more activities of a wildtype ARreceptor, including but not limited to, co-activator binding, DNAbinding, ligand binding, or nuclear translocation. In some embodiments,the first- or second generation-antagonist exhibits decreasedantagonistic activity against a modified AR polypeptide compared to awild type AR polypeptide.

Described herein, in certain embodiments, are methods for determiningwhether a subject is or will become resistant to therapy with a first-or second-generation androgen receptor antagonist, comprising,consisting of, and/or consisting essentially of: (a) testing a samplethat contains a nucleic acid molecule encoding an androgen receptorpolypeptide from the subject to determine whether the encoded androgenreceptor polypeptide is modified at amino acid position 876 of the aminoacid sequence set forth in SEQ ID NO: 1; and (b) characterizing thesubject as resistant or will become resistant to therapy with a first-or second-generation androgen receptor antagonist if the subject has themodification. In some embodiments, the methods further comprise a stepof obtaining the sample from the subject. In some embodiments, thesubject has been administered a first- or second-generation ARantagonist for the treatment of a cancer. In some embodiments, thecancer is a prostate cancer, breast cancer, liver (i.e. hepatocellular)cancer, or bladder cancer. In some embodiments, the cancer is prostatecancer. In some embodiments, the cancer is a castration-resistantprostate cancer. In some embodiments, the methods further comprise,consists of, and/or consists essentially of discontinuing treatment withthe first- or second-generation androgen receptor antagonist if thesample from the subject has the modification at position 876 of SEQ IDNO: 1. In some embodiments, the method further comprises, consists of,and/or consists essentially of continuing treatment with a first- orsecond-generation androgen receptor antagonist if the sample from thesubject does not have the modification at position 876 of SEQ ID NO: 1.In some embodiments, the method further comprises, consists of, and/orconsists essentially of administering a third-generation androgenreceptor antagonist that inhibits the modified AR if the sample fromsubject has the modification at position 876 of SEQ ID NO: 1. In someembodiments, the second-generation androgen receptor antagonist isselected from among ARN-509, enzalutamide (MDV3100), and RD162. In someembodiments, the first-generation androgen receptor antagonist isselected from among bicalutamide, flutamide, hydroxyflutamide ornilutamide.

Described herein, in certain embodiments, are methods for selecting asubject for therapy with a third-generation androgen receptorantagonist, comprising, consisting of, and/or consisting essentially of:(a) testing a sample that contains a nucleic acid molecule encoding anandrogen receptor polypeptide from the subject to determine whether theencoded androgen receptor polypeptide is modified at amino acid position876 of the amino acid sequence set forth in SEQ ID NO: 1; and (b)characterizing the subject as a candidate for therapy with athird-generation androgen receptor antagonist if the subject has themodification. In some embodiments, the methods further comprise a stepof obtaining the sample from the subject. In some embodiments, themethods further comprise, consists of, and/or consists essentially ofdiscontinuing treatment with the first- or second-generation androgenreceptor antagonist if the sample from the subject has the modificationat position 876 of SEQ ID NO: 1. In some embodiments, the method furthercomprises, consists of, and/or consists essentially of continuingtreatment with a first- or second-generation androgen receptorantagonist if the sample from the subject does not have the modificationat position 876 of SEQ ID NO: 1. In some embodiments, the method furthercomprises, consists of, and/or consists essentially of administering athird-generation androgen receptor antagonist that inhibits the modifiedAR if the sample from subject has the modification at position 876 ofSEQ ID NO: 1. In some embodiments, the second-generation androgenreceptor antagonist is selected from among ARN-509, enzalutamide(MDV3100), and RD162. In some embodiments, the first-generation androgenreceptor antagonist is selected from among bicalutamide, flutamide,hydroxyflutamide or nilutamide.

Described herein, in certain embodiments, are methods for characterizinga subject's androgen receptor to determine whether such subject may beresistant to inhibition with a first- or second-generation androgenreceptor antagonist, comprising, consisting of, and/or consistingessentially of: (a) testing a sample that contains a nucleic acidmolecule encoding an androgen receptor polypeptide from the subject todetermine whether the encoded androgen receptor polypeptide is modifiedat amino acid position 876 of SEQ ID NO: 1; and (b) if the subject hasthe modification at position 876 of SEQ ID NO: 1, characterizing theandrogen receptor of the subject as being resistant to inhibition with afirst- or second-generation androgen receptor antagonist. In someembodiments, the methods further comprise a step of obtaining the samplefrom the subject. In some embodiments, the first- or secondgeneration-antagonist exhibits decreased antagonistic activity against amodified AR polypeptide compared to a wild type AR polypeptide. In someembodiments, the methods further comprise, consists of, and/or consistsessentially of discontinuing treatment with the first- orsecond-generation androgen receptor antagonist if the sample from thesubject has the modification at position 876 of SEQ ID NO: 1. In someembodiments, the method further comprises, consists of, and/or consistsessentially of continuing treatment with a first- or second-generationandrogen receptor antagonist if the sample from the subject does nothave the modification at position 876 of SEQ ID NO: 1. In someembodiments, the method further comprises, consists of, and/or consistsessentially of administering a third-generation androgen receptorantagonist that inhibits the modified AR if the sample from subject hasthe modification at position 876 of SEQ ID NO: 1. In some embodiments,the second-generation androgen receptor antagonist is selected fromamong ARN-509, enzalutamide (MDV3100), and RD162. In some embodiments,the first-generation androgen receptor antagonist is selected from amongbicalutamide, flutamide, hydroxyflutamide or nilutamide.

Described herein, in certain embodiments, are methods for monitoringwhether a subject receiving a first- or second-generation androgenreceptor antagonist for treatment of a cancer has developed or willdevelop resistance to the therapy, comprising: (a) testing a sample thatcontains a nucleic acid molecule encoding an androgen receptorpolypeptide from the subject to determine whether the encoded androgenreceptor polypeptide is modified at amino acid position 876 of SEQ IDNO: 1; and (b) characterizing the subject as resistant or will becomeresistant to therapy with a first- or second-generation androgenreceptor antagonist if the subject has the modification. In someembodiments, the methods further comprise a step of obtaining the samplefrom the subject. In some embodiments, the methods further comprise,consists of, and/or consists essentially of discontinuing treatment withthe first- or second-generation androgen receptor antagonist if thesample from the subject has the modification at position 876 of SEQ IDNO: 1. In some embodiments, the method further comprises, consists of,and/or consists essentially of continuing treatment with a first- orsecond-generation androgen receptor antagonist if the sample from thesubject does not have the modification at position 876 of SEQ ID NO: 1.In some embodiments, the method further comprises, consists of, and/orconsists essentially of administering a third-generation androgenreceptor antagonist that inhibits the modified AR if the sample fromsubject has the modification at position 876 of SEQ ID NO: 1. In someembodiments, the second-generation androgen receptor antagonist isselected from among ARN-509, enzalutamide (MDV3100), and RD162. In someembodiments, the first-generation androgen receptor antagonist isselected from among bicalutamide, flutamide, hydroxyflutamide ornilutamide.

Described herein, in certain embodiments, are methods for optimizing thetherapy of a subject receiving a first- or second-generation androgenreceptor antagonist for treatment of a cancer, comprising, consistingof, and/or consisting essentially of: (a) testing a sample that containsa nucleic acid molecule encoding an androgen receptor polypeptide fromthe subject to determine whether the encoded androgen receptorpolypeptide is modified at amino acid position 876 of SEQ ID NO: 1; and(c)(i) if the sample has the modification, discontinuing treatment ofthe subject with the first- or second-generation androgen receptorantagonist or (ii) if the sample does not have the modification,continuing treatment of the subject with the first- or second-generationandrogen receptor antagonist if the subject does not have themodification. In some embodiments, the methods further comprise a stepof obtaining the sample from the subject. In some embodiments, themethods further comprise, consists of, and/or consists essentially ofdiscontinuing treatment with the first- or second-generation androgenreceptor antagonist if the sample from the subject has the modificationat position 876 of SEQ ID NO: 1. In some embodiments, the method furthercomprises, consists of, and/or consists essentially of continuingtreatment with a first- or second-generation androgen receptorantagonist if the sample from the subject does not have the modificationat position 876 of SEQ ID NO: 1. In some embodiments, the method furthercomprises, consists of, and/or consists essentially of administering athird-generation androgen receptor antagonist that inhibits the modifiedAR if the sample from subject has the modification at position 876 ofSEQ ID NO: 1. In some embodiments, the second-generation androgenreceptor antagonist is selected from among ARN-509, enzalutamide(MDV3100), and RD162. In some embodiments, the first-generation androgenreceptor antagonist is selected from among bicalutamide, flutamide,hydroxyflutamide or nilutamide.

In some embodiments, the modified AR polypeptide comprises, consists of,and or consists essentially of a substitution or a deletion of the aminoacid at position 876 of SEQ ID NO: 1. In some embodiments, the modifiedAR polypeptide comprises, consists, and/or consists essentially of asubstitution of phenylalanine to an amino acid selected from the groupconsisting of leucine, isoleucine, valine, alanine, glycine, methionine,serine, threonine, cysteine, tryptophan, lysine, arginine, histidine,proline, tyrosine, asparagine, glutamine, aspartic acid and glutamicacid at position 876 of SEQ ID NO: 1. In some embodiments, the modifiedAR polypeptide comprises, consists of, and/or consists essentially of asubstitution of phenylalanine to an amino acid selected from amongglycine, alanine, valine, leucine, and isoleucine at position 876 of SEQID NO: 1. In some embodiments, the modified AR polypeptide comprises,consists of, and/or consists essentially of a substitution ofphenylalanine to leucine at position 876 of SEQ ID NO: 1. In someembodiments, the modified AR polypeptide comprises, consists of, and/orconsists essentially of a deletion of nucleic acid encoding amino acidposition 876 of SEQ ID NO: 1.

In some embodiments, the nucleic acid encoding the modified ARpolypeptide has (i) a mutation of thymine (t) to cytosine (c) at anucleic acid position corresponding to nucleic acid position 2626 in thesequence of nucleotides set forth in SEQ ID NO: 18; (ii) a mutation ofcytosine (c) to adenine (a) at nucleic acid position corresponding tonucleic acid position 2628 in the sequence of nucleotides set forth inSEQ ID NO: 18; or (ii) a mutation of cytosine (c) to guanine (g) atnucleic acid position corresponding to nucleic acid position 2628 in thesequence of nucleotides set forth in SEQ ID NO: 18.

In some embodiments of the method, the nucleic acid sample is RNA orDNA. In some embodiments of the method, the nucleic acid sample isgenomic DNA. In some embodiments, the method further comprises, consistsof, and/or consists essentially of isolating mRNA from the RNA sample.In some embodiments, the nucleic acid is isolated from a tumor cellsample obtained from the subject. In some embodiments, the sample is atumor biopsy sample, a blood sample, a serum sample, a lymph sample, ora bone marrow aspirate obtained from the subject. In some embodiments,the sample contains circulating tumor cells. In some embodiments, thesample contains disseminated tumor cells. In some embodiments, thenucleic acid is purified from the sample prior to testing. In someembodiments, the nucleic acid is amplified prior to testing.

In some embodiments of the method, testing comprises, consists of,and/or consists essentially performing polymerase chain reaction (PCR)amplification of a nucleic acid sample encoding position 876 of SEQ IDNO: 1. In some embodiments, PCR amplification comprises, consists of,and/or consists essentially of using a pair of oligonucleotide primersthat flank the region encoding amino acid position 876 of SEQ ID NO: 1.In some embodiments, the method further comprises sequencing the PCRamplified nucleic acid using techniques known to those skilled in theart.

In some embodiments, testing comprises, consists of, and/or consistsessentially of contacting the nucleic acid with a sequence specificnucleic acid probe, wherein the sequence specific nucleic acid probe:(a) binds to nucleic acid encoding a modified receptor that is modifiedat amino acid position 876; and (b) does not bind to nucleic acidencoding the wild-type receptor having phenylalanine at position 876 ofSEQ ID NO: 1.

In some embodiments, the first- or second-generation androgen receptorantagonist inhibits a wild-type androgen receptor polypeptide bycompetitive antagonism. In some embodiments, the second-generationandrogen receptor antagonist is selected from among ARN-509,enzalutamide (MDV3100), or RD162.

In some embodiments, the subject has a disease or disorder selected fromamong cancer, an inflammatory disorder or a proliferative disorder. Insome embodiments, the subject has cancer. In some embodiments, thesubject has an AR-mediated cancer. In some embodiments, the cancer isselected from a prostate cancer, a breast cancer, liver (i.e.,hepatocellular) cancer, or a bladder cancer. In some embodiments, thecancer is prostate cancer.

In some embodiments, the subject has a castration resistant prostatecancer. In some embodiments, the subject has a solid tumor.

In some embodiments, the subject is treated with the first- orsecond-generation androgen receptor antagonist prior to obtaining thesample from the subject. In some embodiments, the subject is responsivethe treatment with the first- or second-generation androgen receptorantagonist when it is first administered. In some embodiments, thesample for use in the methods is a sample obtained at 1 week, 2 weeks, 3weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7months, 8 months, 9 months, 10 months, 11 months, 12 months, 14 months,16 months, 18 months, 20 months, 22 months, or 24 months following thefirst administration of with the first- or second-generation ARantagonist. In some embodiments, the sample is obtained 1, 2, 3, 4, 5,6, 7, 8, 9, 10 times over the course of treatment with the first- orsecond-generation AR antagonist. In some embodiments, the subject isresponsive the treatment with the first- or second-generation ARantagonist when it is first administered.

Described herein, in certain embodiments, are methods for screeningcompounds that antagonize a modified androgen receptor, comprising,consisting of and/or consisting essentially of: (a) expressing amodified androgen receptor in a cell, wherein the modified androgenreceptor is modified at an amino acid position corresponding to position876 of SEQ ID NO: 1; (b) contacting the cell with a test compound; and(c) detecting the level of androgen receptor activity in the cell,wherein a decrease in activity expressed indicates that the compoundantagonizes the modified AR. In some embodiments, the test compoundexhibits full antagonist activity toward the modified AR. In someembodiments, the test compound does not exhibit agonist activity towardthe modified AR. Described herein, in certain embodiments, is athird-generation androgen receptor inhibitor identified by the methodsdescribed herein. In some embodiments, the modification of the ARpolypeptide used in the method is a substitution or deletion of theamino acid at position 876 of the androgen receptor polypeptide. In someembodiments, the modification of the AR polypeptide used in the methodis a substitution of phenylalanine to an amino acid selected from amongleucine, isoleucine, valine, alanine, glycine, methionine, serine,threonine, cysteine, tryptophan, lysine, arginine, histidine, proline,tyrosine, asparagine, glutamine, aspartic acid and glutamic acid atamino acid position 876 of the androgen receptor polypeptide. In someembodiments, the modification of the AR polypeptide used in the methodis a substitution of phenylalanine to an amino acid selected from amongglycine, alanine, valine, leucine, and isoleucine at amino acid position876 of the androgen receptor polypeptide. In some embodiments, themodification of the AR polypeptide used in the method is a substitutionof phenylalanine to leucine at amino acid position 876 of the androgenreceptor polypeptide.

In some embodiments, the cell employed in the method is deficient forthe expression of wild-type androgen receptor, expresses a low level ofwild-type androgen receptor, or expresses a modified AR receptor. Insome embodiments, the cell is a selected from among HeLa. CV1, COS7,HepG2, HEK-293, DU145, PC3, TSY-PR1, LNCaP, CWR, VCaP and LAPC4. In someembodiments, the cell comprises a reporter gene operably linked to anandrogen responsive promoter. In some embodiments, the activity of theAR polypeptide is determined by analyzing the expression of the reportergene. In some embodiments, the promoter comprises androgen responseelement. In some embodiments, the androgen response element is 4XARE ora probasin element. In some embodiments, the promoter is a probasin, aprostate specific antigen, MMTV LTR, FASN, STEAP4, TMPRSS2, ORM1, orNKX3.1 promoter. In some embodiments, the reporter gene encodes aprotein selected from among a luciferase, a fluorescent protein, abioluminescent protein, or an enzyme.

Described herein, in certain embodiments, is an isolated androgenreceptor polypeptide or a variant thereof having androgen receptoractivity comprising a modification at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1, wherein the modification confers resistance to anandrogen receptor antagonist on the modified androgen receptorpolypeptide or variant. In some embodiments, the modification comprisessubstitution of the amino acid at position 876 compared to a wild-typeandrogen receptor set forth in SEQ ID NO: 1. In some embodiments, thesubstitution is F876L. In some embodiments, the modification comprises adeletion of amino acid position 876. In some embodiments, the modifiedAR polypeptide has the sequence of amino acids set forth in SEQ ID NO:5. In some embodiments, the modified AR polypeptide is a recombinantpolypeptide. In some embodiments, the modified AR polypeptide comprisesa substitution of the amino acid at position 876 compared to a wild-typeandrogen receptor set forth in SEQ ID NO: 1 and one or more additionalamino acid substitutions. In some embodiments, the modified ARpolypeptide comprises a substitution at amino acid at position 876 thatis F876L. In some embodiments, the modified AR polypeptide comprises oneor more additional amino acid substitutions selected from among one ormore amino acid substitutions associated with castration resistantprostate cancer. In some embodiments, the one or more additional aminoacid substitutions is selected from among one or more substitutions atamino acid positions 701, 741, 874 and 877 compared to a wild-typeandrogen receptor set forth in SEQ ID NO: 1. In some embodiments, theone or more additional amino acid substitutions is selected from amongT877A, W741C, W741L. W741R, L701H and H874Y. In some embodiments, themodified AR polypeptide is a recombinant polypeptide. In someembodiments, the modified AR polypeptide comprises a sequence of aminoacids set forth in SEQ ID NO: 5 or a variant that has at least or atleast about 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96/%, 97%, 98%, 99% ormore sequence identity with the polypeptide having the sequence setforth in SEQ ID NO: 5, wherein the amino acid at position 876 is notphenylalanine.

Described herein, in certain embodiments, is an isolated nucleic acidmolecule encoding the modified androgen receptor polypeptide providedherein. In some embodiments, the nucleic acid is a DNA or an RNAmolecule. In some embodiments, the nucleic acid is a cDNA molecule. Insome embodiments, the nucleic acid is a PCR amplification product. Insome embodiments, the nucleic acid is a recombinant molecule. In someembodiments, the nucleic acid is a synthetic molecule. In someembodiments, the nucleic acid comprises the sequence of nucleic acidsset forth in SEQ ID NO: 19 or a variant that has at least or at leastabout 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or moresequence identity with the polypeptide having the sequence set forth inSEQ ID NO: 19, wherein the nucleic acid codon encoding amino acid atposition 876 does not encode phenylalanine.

Described herein, in certain embodiments, is a vector, comprising anucleic acid molecule encoding the modified androgen receptorpolypeptide provided herein. In some embodiments, the vector is a viralor plasmid vector. In some embodiments, the nucleic acid is operablylinked to a promoter. In some embodiments, the promoter is aconstitutive or an inducible promoter. Described herein, in certainembodiments, is a host cell, comprising the vector. In some embodiments,the cell is a prokaryotic cell or a eukaryotic cell. Described herein,in certain embodiments, is a mutant AR polypeptide expressed by the hostcell.

Described herein, in certain embodiments, is a pharmaceuticalcomposition comprising a third-generation androgen receptor inhibitoridentified by the methods provided herein and a pharmaceuticallyacceptable excipient. Described herein, in certain embodiments, are usesof a third-generation androgen receptor inhibitor identified by themethods provided herein for the manufacture of a medicament. Describedherein, in certain embodiments, are methods of treatment comprisingadministering to a subject in need thereof a therapeutically effectiveamount of the pharmaceutical composition, wherein the compositioncomprises a suitable pharmaceutical carrier. In some embodiments, thesubject has cancer. In some embodiments, the subject has an AR-mediatedcancer. In some embodiments, the cancer is a prostate cancer, breastcancer, liver (i.e. hepatocellular) cancer or bladder cancer. In someembodiments, the cancer is a castration resistant prostate cancer. Insome embodiments, the subject expresses a mutant AR. In someembodiments, the mutant AR comprises a substitution or a deletion of theamino acid at amino acid position 876 in the androgen receptorpolypeptide. In some embodiments, the substitution is F876L. In someembodiments, the third-generation AR antagonist is administered with anadditional therapeutic agent. In some embodiments, the third-generationAR antagonist and the additional therapeutic agent are administeredsequentially, simultaneously or intermittently. In some embodiments, theadditional therapeutic agent is selected from among hormones, hormonereceptor agonists or antagonists, corticosteroids, anti-emetic agents,analgesics, anti-cancer agents, anti-inflammatory agents, kinaseinhibitors, HSP90 inhibitors, histone deacetylase (HDAC) inhibitors. Insome embodiments, the additional therapeutic agent is agonadotropin-releasing hormone (GnRH) agonist or antagonist. In someembodiments, the GnRH agonist is leuprolide, bruserelin or goserelin.

Described herein, in certain embodiments, is a microchip comprising themutant AR polypeptide provided herein or a nucleic acid encodingmodified AR polypeptide provided herein. In some embodiments, themodified AR polypeptide comprises a modification at amino acid 876. Insome embodiments, the modification is an amino acid substitution that isF876L.

Described herein, in certain embodiments, are kits comprising the mutantAR polypeptide provided herein. Described herein, in certainembodiments, is a kit comprising the isolated nucleic acid encoding amutant AR polypeptide provided herein. Described herein, in certainembodiments, are kits comprising one or more reagents for the detectionof a mutant AR polypeptide comprising a modification at amino acidposition 876. Described herein, in certain embodiments, is a kitcomprising one or more reagents for the detection of nucleic acidencoding a mutant AR polypeptide comprising a modification at amino acidposition 876. In some embodiments, the modification is an amino acidsubstitution that is F876L. In some embodiments, the kits comprises apair oligonucleotide primers that flank the nucleic acid region encodingamino acid 876 of a AR polypeptide. In some embodiments, the kitscomprises an oligonucleotide primer that (a) binds to nucleic acidencoding a modified AR that is modified at amino acid position 876; and(b) does not bind to nucleic acid encoding the wild-type AR havingphenylalanine at amino acid position 876. In some embodiments, the kitscomprises a microchip comprising (a) a modified AR polypeptide having amodification that is F876S, or a portion thereof comprising amodification that is F876S; or (b) a nucleic acid molecule encoding amutant AR polypeptide having a modification that is F876S, or a portionthereof comprising a modification that is F876S.

Described herein, in certain embodiments, are systems for detecting amodified AR that is resistant to inhibition with an a first- orsecond-generation AR antagonist in a subject, comprising: (a) a samplecontaining a nucleic acid molecule encoding a AR polypeptide from thesubject; and (b) a microarray comprising nucleic acid encoding a mutantAR polypeptide or a portion thereof that is modified at an amino acidposition corresponding to amino acid position 876 of the amino acidsequence set forth in SEQ ID NO: 1. In some embodiments, the microarrayis contained on a microchip. Described herein, in certain embodiments,are systems for detecting a modified AR that is resistant to inhibitionwith a first- or second-generation AR antagonist in a subject,comprising: (a) a sample containing a nucleic acid molecule encoding aAR polypeptide from the subject; and (b) a sequence specific nucleicacid probe, wherein the sequence specific nucleic acid probe: (i) bindsto nucleic acid encoding a modified AR that is modified at amino acidposition 876; and (ii) does not bind to nucleic acid encoding thewild-type AR having phenylalanine at amino acid position 876. Describedherein, in certain embodiments, are systems for detecting a modified ARthat is resistant to inhibition with a first- or second-generation ARantagonist in a subject, comprising: (a) a sample containing a nucleicacid molecule encoding a AR polypeptide from the subject; and (b) a pairoligonucleotide primers that flank the nucleic acid region encodingamino acid 876 of a AR polypeptide.

Described herein, in certain embodiments, are isolated antibodies thatbind to a modified androgen receptor polypeptide provided herein,wherein the antibody does not bind to or binds with lower affinity to awild-type AR polypeptide having the sequence of amino acids set forth inSEQ ID NO: 1. In some embodiments, the modified AR polypeptide comprisesa modification at amino acid 876. In some embodiments, the modificationis an amino acid substitution that is F876L.

Described herein, in certain embodiments, are methods for maintenancetherapy in a patient having a cancer, comprising: (a) administering tothe patient a maintenance therapy regimen comprising administering atherapeutically effective dose of first- or second-generation ARantagonist; and (b) monitoring the patient at predetermined intervals oftime over the course of the maintenance therapy regimen to determinewhether the subject has mutation in an endogenous gene encoding AR thatresults in a modification at an amino acid position corresponding toamino acid position 876 of the amino acid sequence set forth in SEQ IDNO: 1. In some embodiments, monitoring comprises: testing a samplecontaining a nucleic acid molecule encoding a AR polypeptide from thesubject to determine whether the encoded AR polypeptide is modified atan amino acid position corresponding to amino acid position 876 of theamino acid sequence set forth in SEQ ID NO: 1. In some embodiments, themethods further comprise discontinuing maintenance therapy regimen ifthe subject has the mutation or continuing maintenance therapy regimenif the subject does not have the modification. In some embodiments, themethods further comprise administering third-generation AR antagonistthat inhibits the modified AR if the subject has the modification. Insome embodiments, the modification in the AR polypeptide is F876L. Insome embodiments, the first- or second-generation AR antagonist inhibitsa wild-type AR polypeptide by competitive antagonism. In someembodiments, the second-generation AR antagonist is selected from amongARN-509, enzalutamide (MDV3100), and RD162. In some embodiments, thecancer is a prostate cancer, a breast cancer, a bladder cancer, or ahepatocellular cancer. In some embodiments, the cancer is prostatecancer. In some embodiments, the cancer is a castration resistantprostate cancer. In some embodiments, the predetermined interval of timeis every week, every month, every 2 months, every 3 months, every 4months, every 5 months, every 6 months, every 7 months, every 8 months,every 9 months, every 10 months, every 11 months, or every year.

Other objects, features and advantages of the polypeptides, nucleicacids, compounds, methods and compositions described herein will becomeapparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating specific embodiments, are given by way ofillustration only, since various changes and modifications within thespirit and scope of the instant disclosure will become apparent to thoseskilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-D illustrate ARN-509 and enzalutamide resistance. FIG. 1A showsLNCaP and LNCaP ARN-509r1 cell proliferation. LNCaP and LNCaP ARN-509r1cells were cultured in the presence of hormone depleted medium for 2days followed by ligand addition. Proliferation is quantified byCellTiter-Glo® (Promega Corp.) luminescence based viability assay after7 day compound treatment. FIG. 1B is an agonist proliferation assay ofLNCaP/AR-Luc, LNCaP/AR-LucENZr2 and LNCaP ARN-509r2 cell lines. Cellswere cultured in the presence of hormone depleted medium for 2 daysfollowed by ligand treatment for 7 days. Proliferation is quantified byCellTiter-Glo® luminescence based viability assay. FIG. 1C is anantagonist proliferation assay of parental and 2nd generationanti-androgen resistant cell lines. Cells were cultured in the presenceof hormone depleted medium for 2 days followed by ligand treatment inthe presence of R1881 (final concentration=100 pM). Proliferation isquantified by CellTiter-Glo luminescence based viability assay. FIG. 1Dis a schematic representation of AR domain structure showing amino acidsthat when mutated display altered ligand activity in CRPC.

FIG. 2 illustrates AR levels in parental and 2nd generationanti-androgen resistant cell lines. Protein extracts were generated fromcells cultured in hormone depleted medium for 3 days. AR protein levelswere analyzed and by western blot. AR levels were quantified andnormalized to α-tubulin and expressed relative to LNCaP cells.

FIGS. 3A-B illustrate ARN-509 and enzalutamide are partial agonists ofAR F876L. FIG. 3A shows transcriptional agonist and antagonist activityof ARN-509 and enzalutamide on wild-type or F876L AR. Transcriptionalactivation of a 4X ARE-luciferase reporter was measured in the presenceof increasing compound concentration in the absence or presence of 1 nMR1881 (for wild-type AR) or 5 nM R1881 (for F876L AR). FIG. 3B showstranscriptional agonist activity of 1st and 2^(nd) generationanti-androgens and prednisone on wild-type, F876L, T877A. F876L/T877A,L701H, H874Y and W741C AR dependent activation of 4X ARE-Luciferasereporter was measured in transiently transfected HepG2 cells.

FIGS. 4A-B illustrate VP16-AR (FIG. 4A) and F876L VP16-AR (FIG. 4B)agonist and antagonist activity of ARN-509 and enzalutamide. 4XARE-luciferase reporter activity was monitored in the presence ofincreasing compound concentration in the absence or presence of 90 pMR1881 (for wild-type VP16-AR) or 1 nM R1881 (for F876L VP16-AR).

FIGS. 5A-B illustrate a competitive binding assay of wild-type AR (FIG.5A) vs. F876L AR (FIG. 5B). 3H-R1881 binding performed in PC3 cellextracts expressing wild-type or F876L AR. Data is representative of 3independent experiments. Error bars, SEM; n=2.

FIG. 6 illustrates AR levels in AR overexpressing cell lines. Proteinextracts were generated from LNCaP, LNCap/AR(cs), LNCaP/SRαF876L andLNCaP/pCDNAF876L cells cultured in hormone depleted medium for 3 days.AR protein levels were analyzed and by Western blot. AR levels werequantified and normalized to actin and expressed relative to LNCaPcells.

FIGS. 7A-B illustrate that the F876L AR mutation confers partial agonistactivity to ARN-509 and enzalutamide. FIG. 7A shows LNCaP/AR(cs) andLNCaP/SRαF876L cell proliferation. Cells were cultured in the presenceof hormone depleted medium for 2 days followed by ligand treatment for 7days. Proliferation is quantified by CellTiter-Glo luminescence basedviability assay. FIG. 7B shows LNCaP/AR(cs), LNCaP/SRαF876L andLNCaP/pCDNAF876L cell proliferation. Cells were cultured in hormonedepleted medium for 2 days followed by ligand treatment for 7 days. Forantagonist assays, compounds were added in the presence of 200 pM R1881(100 pM final concentration). Proliferation was quantified using theluminescence based CellTiter-Glo® assay.

FIG. 8 illustrates AR N/C interaction assay. Ligand induced N/Cinteraction was monitored via mammalian two hybrid assay in HepG2 cells.Antagonists were assayed at 8 μM, R1881 at 1 nM.

FIG. 9 illustrates AR ChIP analysis of AR target genes. ChIP assays wereperformed on LNCaP/AR(cs) and LNCaP/SRαF876L cells incubated for 3 daysin hormone depleted medium followed by 4 hour ligand treatment. Cellswere treated in with 10 μM antagonist in the presence or absence of 1 nMR1881. Data for AR and non-specific IgG control is presented as percentinput.

FIG. 10 illustrates AR F876L mutation confers ARN-509 and enzalutamideresistance in vivo. LNCaP/AR(cs) and LNCaP/SRαF876L tumor xenografts.Castrate male mice bearing tumors were treated daily with vehicle or 30mg/kg/day compound. Tumor growth for each group is presented as theaverage tumor volume±SEM.

FIG. 11 illustrates the dosing schedule for the open-label phase ½safety, pharmacokinetic, and proof-of-concept study of ARN-509 inpatients with progressive advanced, metastatic Castration-ResistantProstate Cancer.

FIGS. 12A-B illustrate identification of AR-F876L in ARN-509 treatedpatients. FIG. 12A shows PSA response of 29 patients analyzed for F876Lmutation. Terminal end of PSA response line is time at which the patientplasma was screened for F876L mutation using BEAMing analysis. Theplasma used in this study was initially collected to determinepharmacokinetics of ARN-509 and as such the samples were not preparedusing methodology to maximize ratio of ctDNA to lymphocyte DNA. FIG. 12Bshows PSA response of patient positive for F876L. PSA response ofpatient 7 at indicated treatment cycle. Circulating plasma was analyzedfor the F876L at times indicated with arrows. The plasma samples with nodetectable mutant are notated as “w.t.”, the presence of the F876Lmutation is represented by “m”. A plasma sample was called positive forthe mutant if the percent of mutant beads was above the cut-off (0.02%)and the number of mutant copies estimated to be ≧0.5 (number of genomeequivalents in the plasma sample x mutant bead fraction=≧0.5).

FIG. 13 illustrates the relative amount of prostate specific antigen(PSA) detected over the course of the Phase ½ ARN-509 clinical study ineach of the three patients (7, 10, and 13) bearing detectable somaticF876L mutations in AR. Arrow indicates sample in which the mutation(s)were detected.

DETAILED DESCRIPTION OF THE INVENTION Certain Terminology

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as is commonly understood by one of skill in theart to which the claimed subject matter belongs. All patents, patentapplications, published applications and publications, GENBANKsequences, websites and other published materials referred to throughoutthe entire disclosure herein, unless noted otherwise, are incorporatedby reference in their entirety. In the event that there is a pluralityof definitions for terms herein, those in this section prevail. Wherereference is made to a URL or other such identifier or address, it isunderstood that such identifiers can change and particular informationon the internet can come and go, but equivalent information is known andcan be readily accessed, such as by searching the internet and/orappropriate databases. Reference thereto evidences the availability andpublic dissemination of such information. Generally, the procedures forcell culture, cell infection, antibody production and molecular biologymethods are methods commonly used in the art. Such standard techniquescan be found, for example, in reference manual, such as, for example,Sambrook et al. (2000) and Ausubel et al. (1994).

As used herein, the singular forms “a,” “an” and “the” include pluralreferents unless the context clearly dictates otherwise. In thisapplication, the use of the singular includes the plural unlessspecifically stated otherwise. As used herein, the use of “or” means“and/or” unless stated otherwise. Furthermore, use of the term“including” as well as other forms (e.g., “include”, “includes”, and“included”) is not limiting.

As used herein, ranges and amounts can be expressed as “about” aparticular value or range. About also includes the exact amount. Hence“about 5 μg” means “about 5 μg” and also “5 μg.” Generally, the term“about” includes an amount that would be expected to be withinexperimental error.

As used herein, an androgen receptor (AR) polypeptide refers to anyandrogen receptor protein or polypeptide, including, but not limited to,a recombinantly produced protein, a synthetically produced protein, anative androgen receptor protein, and an androgen receptor proteinextracted from cells or tissues. An AR polypeptide includes relatedpolypeptides from different species including, but not limited toanimals of human and non-human origin. AR polypeptides of non-humanorigin include, but are not limited to, non-human primate (e.g.chimpanzee and ape), murine (e.g., mouse and rat), canine (dog), feline(cat), leporine (rabbit), avian (bird), bovine (cow), ovine (sheep),porcine (pig), equine (horse), piscine (fish), ranine (frog) and othermammalian or non-mammalian AR polypeptides. Exemplary AR polypeptidesinclude, for example, SEQ ID NOS: 1-17. An androgen receptor polypeptideincludes wild-type androgen receptor, allelic variant isoforms, somaticmutations including those found in tumors, synthetic molecules fromnucleic acids, protein isolated from human tissue and cells, andmodified forms thereof. The androgen receptor polypeptides providedherein can be further modified by modification of the primary amino acidsequence, by deletion, addition, or substitution of one or more aminoacids. An androgen receptor polypeptide includes any AR polypeptide or aportion thereof having AR activity, including for example, fusionpolypeptides of an AR ligand binding domain to a heterologous DNAbinding domain.

As used herein, a mutant androgen receptor (AR) polypeptide, a mutant ARprotein, a modified AR polypeptide, or a modified AR protein or are usedinterchangeably herein and refer to an androgen receptor polypeptidethat is modified at one or more amino acid positions. Exemplarymodifications include, but are not limited to, substitutions, deletionsor additions of amino acids.

As used herein, the term “anti-androgen” refers to a group of hormonereceptor antagonist compounds that are capable of preventing orinhibiting the biologic effects of androgens on normally responsivetissues in the body.

As used herein, the term “AR inhibitor” or “AR antagonist” are usedinterchangeably herein and refer to an agent that inhibits or reduces atleast one activity of an AR polypeptide. Exemplary AR activitiesinclude, but are not limited to, co-activator binding, DNA binding,ligand binding, or nuclear translocation.

As used herein, a “full antagonist” refers to an antagonist which, at aneffective concentration, essentially completely inhibits an activity ofan AR polypeptide. As used herein, a “partial antagonist” refers anantagonist that is capable of partially inhibiting an activity of an ARpolypeptide, but that, even at a highest concentration is not a fullantagonist. By ‘essentially completely’ is meant at least about 80%, atleast about 90%, at least about 95%, at least about 96%, at least about97%, at least about 98% at least about 99%, or greater inhibition of theactivity of an AR polypeptide.

As used herein, the term “third-generation AR inhibitor” or“third-generation AR antagonist” are used interchangeably herein andrefer to an agent that inhibits at least one activity of an ARpolypeptide containing one or more amino acid modifications that confersresistance to inhibition by a second-generation AR antagonist, such as,for example, ARN-509 (CAS No. 956104-40-8), enzalutamide (also known asMDV3100; CAS No: 915087-33-1), or RD162 (CAS No. 915087-27-3). In someembodiments, a third-generation AR inhibitor inhibits at least oneactivity of a wild-type AR polypeptide, such as, but not limited to,co-activator binding, DNA binding, ligand binding, or nucleartranslocation. In some embodiments, a third-generation AR inhibitorinhibits an activity of a mutant AR polypeptide that is also inhibitedby a first- or second-generation AR inhibitor.

As used herein, the phrase “resistant to inhibition” refers to adecrease in ability of an AR antagonist to inhibit (i.e. antagonize) oneor more activities of a modified AR polypeptide compared to a wild typeAR polypeptide. For example, the AR antagonist is less effective atinhibiting a modified AR polypeptide compared to a wild type ARpolypeptide. In some embodiments, the decreased antagonistic activityagainst a modified AR polypeptide is about 5%, 10%, 20%, 30%, 40%, 50%,60%, 70%, 80%, 85%, 90%, 95%, 98% or 100% compared to the antagonisticactivity against a wildtype AR polypeptide. Exemplary AR activitiesinclude, but are not limited to, co-activator binding, DNA binding,ligand binding, or nuclear translocation. In some embodiments, the ARantagonist is unable to bind to or binds with decreased affinity to amodified AR polypeptide.

As used herein, the term “second-generation AR inhibitor” or“second-generation AR antagonist” are used interchangeably herein andrefer to an agent that exhibits full antagonist activity of a wild-typeAR polypeptide, but does not exhibit full antagonist activity of an ARpolypeptide containing one or more amino acid modifications that confersresistance to inhibition, such as a modification at amino acid position876 in the AR polypeptide. In some embodiments, the second-generation ARinhibitor does not exhibit full antagonist activity on an AR polypeptidehaving an amino acid substitution that is F876L. In some embodiments,the second-generation AR inhibitor induces activity of AR (i.e. is an ARagonist) at concentrations that are equivalent or higher than theconcentration required to inhibit a wild-type AR. Second-generation ARinhibitors differ from first-generation AR inhibitors, such asbicalutamide and flutamide, in that second-generation AR inhibitors actas full antagonists in cells expressing elevated levels of AR, such asfor example, in castration resistant prostate cancers (CRPC).First-generation AR inhibitors, such as bicalutamide and flutamide, actas agonists in CRPC. Exemplary second-generation AR inhibitors includeARN-509, enzalutamide and RD162. In some embodiments, asecond-generation AR inhibitor is an agonist of a mutant AR polypeptideprovided herein. In some embodiments, a second-generation AR inhibitorbinds to an AR polypeptide at or near the ligand binding site of the ARpolypeptide.

The term “nucleic acid” refers to deoxyribonucleotides,deoxyribonucleosides, ribonucleosides, or ribonucleotides and polymersthereof in either single- or double-stranded form. Unless specificallylimited, the term encompasses nucleic acids containing known analogs ofnatural nucleotides which have similar binding properties as thereference nucleic acid and are metabolized in a manner similar tonaturally occurring nucleotides. Unless specifically limited otherwise,the term also refers to oligonucleotide analogs including PNA(peptidonucleic acid), analogs of DNA used in antisense technology(e.g., phosphorothioates, phosphoroamidates). Unless otherwiseindicated, a particular nucleic acid sequence also implicitlyencompasses conservatively modified variants thereof (including but notlimited to, degenerate codon substitutions) and complementary sequencesas well as the sequence explicitly indicated. Specifically, degeneratecodon substitutions are achieved by generating sequences in which thethird position of one or more selected (or all) codons is substitutedwith mixed-base and/or deoxyinosine residues (Batzer et al. (1991)Nucleic Acid Res, 19:5081; Ohtsuka et al. (1985) J. Biol. Chem.260:2605-2608; and Cassol et al. (1992) Mol. Cell. Probes 6, 327-331;and Rossolini et al. (1994) Mol. Cell. Probes 8:91-98).

The term “amino acid” refers to naturally occurring and non-naturallyoccurring amino acids, as well as amino acid analogs and amino acidmimetics that function in a manner similar to the naturally occurringamino acids. Naturally encoded amino acids are the 20 common amino acids(alanine, arginine, asparagine, aspartic acid, cysteine, glutamine,glutamic acid, glycine, histidine, isoleucine, leucine, lysine,methionine, phenylalanine, proline, serine, threonine, tryptophan,tyrosine, and valine) and pyrolysine and selenocysteine. Amino acidanalogs refers to agents that have the same basic chemical structure asa naturally occurring amino acid, i.e., an a carbon that is bound to ahydrogen, a carboxyl group, an amino group, and an R group, such as,homoserine, norleucine, methionine sulfoxide, methionine methylsulfonium. Such analogs have modified R groups (such as, norleucine) ormodified peptide backbones, but retain the same basic chemical structureas a naturally occurring amino acid.

Amino acids are referred to herein by either their commonly known threeletter symbols or by the one-letter symbols recommended by the IUPAC-IUBBiochemical Nomenclature Commission. Nucleotides, likewise, are referredto by their commonly accepted single-letter codes.

The terms “polypeptide”, peptide” and “protein” are used interchangeablyherein to refer to a polymer of amino acid residues. The terms apply tonaturally occurring amino acid polymers as well as amino acid polymersin which one or more amino acid residues is a non-naturally occurringamino acid, e.g., an amino acid analog. The terms encompass amino acidchains of any length, including full length proteins, wherein the aminoacid residues are linked by covalent peptide bonds.

As used herein, modification refers to modification of a sequence ofamino acids of a polypeptide or a sequence of nucleotides in a nucleicacid molecule and includes deletions, insertions, and replacements ofamino acids and nucleotides, respectively.

To determine the percent homology of two amino acid sequences or of twonucleic acids, the sequences can be aligned for optimal comparisonpurposes (e.g., gaps are introduced in the sequence of a first aminoacid or nucleic acid sequence for optimal alignment with a second aminoor nucleic acid sequence). The amino acid residues or nucleotides atcorresponding amino acid positions or nucleotide positions can then becompared. When a position in the first sequence is occupied by the sameamino acid residue or nucleotide as the corresponding position in thesecond sequence, then the molecules are identical at that position. Thepercent homology between the two sequences is a function of the numberof identical positions shared by the sequences (i.e., % identity=# ofidentical positions/total # of positions (e.g., overlappingpositions)×100). In some embodiments the two sequences are the samelength.

To determine percent homology between two sequences, the algorithm ofKarlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264-2268,modified as in Karlin and Altschul (1993) Proc. Natl. Acad Sci. USA90:5873-5877 is used. Such an algorithm is incorporated into the NBLASTand XBLAST programs of Altschul. et al. (1990) J. Mol. Biol.215:403-410. BLAST nucleotide searches are performed with the NBLASTprogram, score=100, wordlength=12 to obtain nucleotide sequenceshomologous to a nucleic acid molecules described or disclose herein.BLAST protein searches are performed with the XBLAST program, score=50,wordlength=3. To obtain gapped alignments for comparison purposes,Gapped BLAST is utilized as described in Altschul et al. (1997) NucleicAcids Res. 25:3389-3402. When utilizing BLAST and Gapped BLAST programs,the default parameters of the respective programs (e.g., XBLAST andNBLAST) are used. See the website of the National Center forBiotechnology Information for further details (on the World Wide Web atncbi.nlm.nih.gov). Proteins suitable for use in the methods describedherein also includes proteins having between 1 to 15 amino acid changes,e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acidsubstitutions, deletions, or additions, compared to the amino acidsequence of any protein described herein. In other embodiments, thealtered amino acid sequence is at least 75% identical, e.g., 77%, 80%,82%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of any protein described herein.Such sequence-variant proteins are suitable for the methods describedherein as long as the altered amino acid sequence retains sufficientbiological activity to be functional in the compositions and methodsdescribed herein. Where amino acid substitutions are made, thesubstitutions should be conservative amino acid substitutions. Among thecommon amino acids, for example, a “conservative amino acidsubstitution” is illustrated by a substitution among amino acids withineach of the following groups: (1) glycine, alanine, valine, leucine, andisoleucine, (2) phenylalanine, tyrosine, and tryptophan, (3) serine andthreonine, (4) aspartate and glutamate, (5) glutamine and asparagine,and (6) lysine, arginine and histidine. Those of skill in this artrecognize that, in general, single amino acid substitutions innon-essential regions of a polypeptide do not substantially alterbiological activity (see, e.g., Watson et al. Molecular Biology of theGene, 4th Edition, 1987, The Benjamin/Cummings Pub. co., p. 224). TheBLOSUM62 table is an amino acid substitution matrix derived from about2,000 local multiple alignments of protein sequence segments,representing highly conserved regions of more than 500 groups of relatedproteins (Henikoff et al (1992) Proc. Natl. Acad. Sci. USA,89:10915-10919). Accordingly, the BLOSUM62 substitution frequencies areused to define conservative amino acid substitutions that, in someembodiments, are introduced into the amino acid sequences described ordisclosed herein. Although it is possible to design amino acidsubstitutions based solely upon chemical properties (as discussedabove), the language “conservative amino acid substitution” preferablyrefers to a substitution represented by a BLOSUM62 value of greater than−1. For example, an amino acid substitution is conservative if thesubstitution is characterized by a BLOSUM62 value of 0, 1, 2, or 3.According to this system, preferred conservative amino acidsubstitutions are characterized by a BLOSUM62 value of at least 1 (e.g.,1, 2 or 3), while more preferred conservative amino acid substitutionsare characterized by a BLOSUM62 value of at least 2 (e.g., 2 or 3).

As used herein, corresponding residues refers to residues that occur ataligned loci. Related or variant polypeptides are aligned by any methodknown to those of skill in the art. Such methods typically maximizematches, and include methods such as using manual alignments and byusing the numerous alignment programs available (for example, BLASTP)and others known to those of skill in the art. By aligning the sequencesof polypeptides, one skilled in the art can identify correspondingresidues, using conserved and identical amino acid residues as guides.Corresponding positions also can be based on structural alignments, forexample by using computer simulated alignments of protein structure. Inother instances, corresponding regions can be identified.

As used herein, an allelic variant or allelic variation references to apolypeptide encoded by a gene that differs from a reference form of agene (i.e. is encoded by an allele). Typically the reference form of thegene encodes a wild-type form and/or predominant form of a polypeptidefrom a population or single reference member of a species. Typically,allelic variants, which include variants between and among species, haveat least 80%, 90% or greater amino acid identity with a wild-type and/orpredominant form from the same species; the degree of identity dependsupon the gene and whether comparison is interspecies or intraspecies.Generally, intraspecies allelic variants have at least about 80%, 85%6,90% or 95% identity or greater with a wild-type and/or predominant form,including 96%, 97%, 98%, 99% or greater identity with a wild-type and/orpredominant form of a polypeptide.

As used herein, species variants refer to variants of the samepolypeptide between and among species. Generally, interspecies variantshave at least about 60/%, 70%, 80%, 85%, 90%, or 95% identity or greaterwith a wild-type and/or predominant form from another species, including96%, 97%, 98%, 99% or greater identity with a wild-type and/orpredominant form of a polypeptide.

As used herein, the terms “treat,” “treating” or “treatment,” and othergrammatical equivalents, include alleviating, abating or amelioratingone or more symptoms of a disease or condition, ameliorating, preventingor reducing the appearance, severity or frequency of one or moreadditional symptoms of a disease or condition, ameliorating orpreventing the underlying metabolic causes of one or more symptoms of adisease or condition, inhibiting the disease or condition, such as, forexample, arresting the development of the disease or condition,relieving the disease or condition, causing regression of the disease orcondition, relieving a condition caused by the disease or condition, orinhibiting the symptoms of the disease or condition eitherprophylactically and/or therapeutically. In a non-limiting example, forprophylactic benefit, a third-generation AR inhibitor compound disclosedherein is administered to an individual at risk of developing aparticular disorder, predisposed to developing a particular disorder, orto an individual reporting one or more of the physiological symptoms ofa disorder. In some embodiments, a third-generation AR inhibitorcompound disclosed herein is administered to a subject followingtreatment with one or more therapeutic agents. In some embodiments, athird-generation AR inhibitor compound disclosed herein is administeredto a subject in combination with treatment with one or more therapeuticagents.

As used herein, prevention or prophylaxis refers to the reduction in therisk of developing a disease or condition.

The terms “effective amount”, “therapeutically effective amount” or“pharmaceutically effective amount” as used herein, refer to an amountof an AR inhibitor compound that is sufficient to treat a disorder. Insome embodiments, the result is a reduction in and/or alleviation of thesigns, symptoms, or causes of a disorder, or any other desiredalteration of a biological system. For example, an “effective amount”for therapeutic uses is the amount of the composition comprising an ARinhibitor compound disclosed herein required to provide a clinicallysignificant decrease in a disorder. An appropriate “effective” amount inany individual case is determined using any suitable technique, (e.g., adose escalation study).

The term “pharmaceutically acceptable” as used herein, refers to amaterial, (e.g., a carrier or diluent), which does not abrogate thebiological activity or properties of an AR inhibitor compound describedherein, and is relatively nontoxic (i.e., the material is administeredto an individual without causing undesirable biological effects orinteracting in a deleterious manner with any of the components of thecomposition in which it is contained).

As used herein, a control refers to a sample that is substantiallyidentical to the test sample, except that it is not treated with a testparameter, or, if it is a plasma sample, it can be from a normalvolunteer not affected with the condition of interest. A control alsocan be an internal control.

As used herein, the terms “subject”, “individual” and “patient” are usedinterchangeably. None of the terms are to be interpreted as requiringthe supervision of a medical professional (e.g., a doctor, nurse,physician's assistant, orderly, hospice worker). As used herein, thesubject can be any animal, including mammals (e.g., a human or non-humananimal) and non-mammals. In one embodiment of the methods andcompositions provided herein, the mammal is a human.

As used herein, “contacting” refers to refers to the act of touching,making contact, or of bringing substances into immediate proximity.“Contacting” can be achieved by mixing the components in a fluid orsemi-fluid mixture.

Overview: AR Function and Drug Resistance in Cancer

Androgen receptor (AR) is a member of the steroid and nuclear receptorsuperfamily. Among this large family of proteins, only five vertebratesteroid receptors are known and include the androgen receptor, estrogenreceptor, progesterone receptor, glucocorticoid receptor, andmineralocorticoid receptor. AR is a soluble protein that functions as anintracellular transcription factor. AR function is regulated by thebinding of androgens, which initiates sequential conformational changesof the receptor that affect receptor-protein interactions andreceptor-DNA interactions.

AR is mainly expressed in androgen target tissues, such as the prostate,skeletal muscle, liver, and central nervous system (CNS), with thehighest expression level observed in the prostate, adrenal gland, andepididymis. AR in certain instance is activated by the binding ofendogenous androgens, including testosterone and 5α-dihydrotestosterone(5α-DHT).

AR is a 110 kD nuclear receptor that, upon activation by androgens,mediates transcription of target genes that modulate growth anddifferentiation of prostate epithelial cells. AR is encoded by the ARgene located on the X chromosome at Xq11-12. The AR gene comprises 8exons encoding the full-length androgen receptor. Similar to the othersteroid receptors, unbound AR is mainly located in the cytoplasm andassociated with a complex of heat shock proteins (HSPs) throughinteractions with the ligand-binding domain. Upon agonist binding, ARgoes through a series of conformational changes: the heat shock proteinsdissociate from AR, and the transformed AR undergoes dimerization,phosphorylation, and translocation to the nucleus, which is mediated bythe nuclear localization signal. The translocated receptor then binds tothe androgen response element (ARE), which is characterized by the twohexameric six-nucleotide half-site consensus sequence 5′-TGTTCT-3′arranged as inverted repeats spaced by three random nucleotides and islocated in the promoter or enhancer region of AR gene targets.Recruitment of other transcription co-regulators (includingco-activators and co-repressors) and transcriptional machinery furtherensures the appropriate modulation of AR-regulated gene expression.These processes are initiated by the ligand-induced conformationalchanges in the ligand-binding domain.

AR signaling is crucial for the development and maintenance of malereproductive organs including the prostate gland, as genetic malesharboring loss of function AR mutations and mice engineered with ARdefects do not develop prostates. This dependence of prostate cells onAR signaling continues even upon neoplastic transformation. Androgendepletion (e.g. using gonadotropin-releasing hormone (GnRH) agonists)continues to be the mainstay of prostate cancer treatment. However,androgen depletion is usually effective for a limited duration andprostate cancer evolves to regain the ability to grow despite low levelsof circulating androgens.

Prostate cancer is the most prevalent cancer in men. Prostate cancerrepresents approximately 29 percent of all new cancer cases diagnosedand 10 percent of cancer deaths in males. In addition, American men overtheir lifetime have a roughly 17 percent chance of developing invasiveprostate cancer. At initial diagnosis, a large percentage of prostatecancers have low to medium risk, meaning that the 10 year mortality riskis relatively low (up to 24%) with little intervention. However,advanced and metastatic prostate cancers have mean survival of 2.5-3years and are subject to aggressive treatment including surgery andchemical castration therapy.

Given that most prostate cancer cells depend on AR for theirproliferation and survival, treatment generally consists ofadministration of agents that block production of testosterone (e.g.GnRH agonists), alone or in combination with anti-androgens (e.g.bicalutamide), which antagonize the effect of any residual testosterone.Unfortunately, while often initially successful as evidenced by a dropin prostate specific antigen (PSA) and regression of visible tumor ifpresent, metastatic tumors inevitably become resistant to hormonaltherapy at which stage no curative treatment exists.

Prostate cancers resistant to hormonal therapies are currently referredto as ‘castration resistant’, implying that they have progressed beyondthe point at which drugs targeting any point on the androgen axis wouldhave any clinical utility. Pre-clinical and clinical evidence indicatethat the AR is a viable therapeutic target even in castration resistantcancers. AR mutations have been reported to occur in up to 33 percent ofprostate cancer cases and are most commonly observed following treatmentin the AR dependent castration resistant state. Mutations have beenfound that alter ligand specificity and potency and that result inligand independent receptor activity. The specific mutations vary widelybut appear to be dependent upon treatment regimen. Additionally,upregulation of the AR itself has been associated with progression tothe castration resistant state in both patients and animal models.

Two agents, abiraterone acetate (Zytiga; CAS No. 154229-19-3) andMDV3100 (enzalutamide; CAS No. 915087-33-7), have recently been employedin late stage clinical testing for the treatment of men withcastration-resistant prostate cancer (CRPC). Abiraterone acetate targets7-α-hydroxylase/17,20-lyase (CYP17A), thereby inhibiting residualandrogen biosynthesis. MDV3100 is an anti-androgen discovered in ascreen for potent anti-androgens lacking agonist activity in context ofAR overexpression. The clinical efficacies of MDV3100 and abirateroneacetate support the hypothesis that AR continues to promote growth andsurvival of castration resistant prostate cancer. Unfortunately, similarto first-generation androgen ablation therapies, prolonged treatmentwith abiraterone acetate or second-generation AR antagonists ultimatelyresults in resistance.

Resistance to abiraterone acetate and MDV3100 has been observed in bothmodels of prostate cancer and in patients. Preliminary data suggeststhat, similar to castration resistant prostate cancer, second-generationanti-androgen resistance develops through multiple mechanisms and AR isthought to remain a therapeutic target in this setting. In bothxenograft models and in patients, CYP17A upregulation and the presenceof picogram levels of androgens have been noted in resistantpopulations. CYP17A upregulation presumably promotes resistance via ARactivation by intratumoral androgen synthesis. In other cases,resistance correlates with increased AR levels as well as nuclearlocalization. Additionally, numerous cellular signaling pathways knownto activate AR in the absence of endogenous ligands may promotesecond-generation therapy resistance. The observation that tumors withhigh levels of activated Src respond poorly to MDV3100 and abirateroneacetate treatment supports this hypothesis. To date, no AR mutationshave been described that confer resistance to MDV3100, ARN-509 orabiraterone.

ARN-509 is a synthetic thiohydantoin compound discovered usingstructure-activity relationship (SAR)-guided medicinal chemistry toidentify nonsteroidal anti-androgens that retain full antagonistactivity in the setting of increased AR expression. ARN-509 exhibitsanti-tumor activity in castration-sensitive and resistant xenograftmodels of prostate cancer and anti-androgenic effects in dogs thatphenocopy castration.

Identification of AR Inhibitor-Resistant Cell Lines and a Mutant ARPolypeptide

Described herein are working examples demonstrating the production ofdrug resistant cell lines. In some embodiments, the methods provided areemployed for the generation of a cell line that is resistant toinhibition by a second-generation-AR antagonist, such as, but notlimited to, ARN-509, enzalutamide (MDV3100) or RD162. In someembodiments, the methods provided are employed for the generation of acell line that is resistant to inhibition by an AR antagonist thatinhibits androgen production and exhibits binding to an AR receptor. Insome embodiments, the AR antagonist that inhibits androgen production isa CYP17A inhibitor and exhibits binding to AR. In some embodiments, theAR antagonist that inhibits androgen production and exhibits AR bindingis galeterone (TOK001) or abiraterone acetate. In some embodiments, theAR antagonist that inhibits androgen production and exhibits AR bindingis TAK-700.

As described herein, resistant cell lines were generated in vivo in acastration resistant prostate cancer (CRPC) cell xenograft and in vitroin androgen responsive prostate cancer cell lines by exposure toincreasing concentrations of the anti-androgen drugs ARN-509 or MDV3100.In cell proliferation and transcriptional assays, the cell linessegregated into two distinct classes.

Class 1 cell lines expressed a higher level of AR compared to theirparental cell lines and proliferated in the absence of added androgens.Ligand-independent growth of the class 1 cells was unaltered in thepresence of ARN-509, MDV3100 or bicalutamide. The synthetic androgen,R1881, inhibited proliferation in the class 1 cells and is antagonizedby either MDV3100 or ARN-509, indicating that AR in these cell linesstill binds to MDV3100 and ARN-509.

Class 2 resistant cell lines remained androgen dependent for growthsimilar to their parental cell lines. While ARN-509 and MDV3100inhibited proliferation of the parental cell line, both compoundsexhibited agonist activity and stimulated proliferation of the class 2cell lines. Analysis of the nucleic acid encoding AR in the class 2 celllines revealed that the cell lines expressed a mutant AR with a mutationin the ligand binding domain. The mutation was a thymidine (T) tocytosine (C) missense mutation that resulted in an amino acidsubstitution of phenylalanine at position 876 of the wild-type AR forleucine (F876L).

As described herein, in the examples, mutations in the AR gene have beenidentified in plasma samples from prostate cancer patients undergoingARN-509 Phase ½ clinical studies. The mutations identified include athymidine (T) to cytosine (C) missense mutation at position 2988 (firstposition of the codon encoding phenylanine, which is encoded in exon 8of the AR gene), and a cytosine (C) to alanine (A) missense mutation atposition 2990 (third position of the codon encoding phenylalanine) in anamino acid substitution of phenylalanine at position 876 of thewild-type AR for leucine (F876L). The patients identified as havingthese mutations also exhibited increasing levels of prostate specificantigen (PSA) over the course of the study indicating increasingresistance to treatment.

Described herein are mutant AR polypeptides that contain an amino acidsubstitution of phenylalanine at position 876 of the wild-type AR forleucine (F876L) and nucleic acids encoding the polypeptides. Alsodescribed herein are methods of producing the mutant AR nucleic acidsand polypeptides described herein. Also described herein arecompositions, combinations and kits containing the mutant AR nucleicacids and polypeptides described herein. Also provided are methods ofusing the mutant AR polypeptides for identifying mutant AR interactingmolecules, including androgen inhibitors, including third-generation ARinhibitor compounds. Also provided are compositions containing themutant AR interacting molecules, including pharmaceutical compositionsthereof. Also provided are methods of treatment using the identifiedmutant AR interacting molecules. Also described herein are mutant ARnucleic acids that are synthetic nucleic acids. Also described hereinare mutant AR nucleic acids that are cDNA molecules. Also describedherein are mutant AR polypeptides produced by mutant AR nucleic acidsthat are synthetic nucleic acids. Also described herein are mutant ARpolypeptides produced by mutant AR nucleic acids that are cDNAmolecules. Also described herein are mutant AR nucleic acids that do notcontain AR genomic DNA. Also described herein are mutant AR nucleicacids that are unmethylated. Also described herein are mutant AR nucleicacids that do not contain AR intron sequences. Also described herein aremutant AR nucleic acids that comprises a sequence of nucleotides fromtwo or more exons of the AR genomic sequence. In some embodiments, themutant AR nucleic acids comprise a sequence of nucleotides that encodephenylalanine at a position corresponding to position 876 of thewild-type AR polypeptide.

As described herein, identification of a mutation at position 876 in theAR, such as for example F876L, allows for the design and screening ofinhibitors effective for inhibition of a mutant AR having one or moreresistance mutations. Such inhibitors are useful in clinical andtherapeutic applications. In some embodiments, the inhibitors are usefulfor the treatment of a cancer, such as for example, an AR-mediatedcancer, such as, for example, a prostate cancer, breast cancer, liver(i.e. hepatocellular) cancer, or bladder cancer, such as for example, adrug resistant prostate, breast, liver (i.e. hepatocellular), or bladdercancer.

As described herein, in some embodiments, subjects are screened for theidentification of a mutation at position 876 in AR, such as for exampleF876L. In some embodiments, identification of such a mutation allows forthe prescription of a cancer treatment or modification of a cancertreatment. In some embodiments, identification of such a mutation isused to stratify subjects for a particular therapy, such as for example,therapy with an inhibitor that inhibits the activity of the mutant AR(i.e. a third-generation AR inhibitor). In some embodiments,identification of such a mutation is used to characterize a subject ashaving a high risk of relapse of a disease or condition, such as, forexample, a prostate cancer, breast cancer, liver (i.e. hepatocellular)cancer, or bladder cancer. In some embodiments, identification of such amutation is used to characterize a subject as lacking responsiveness toparticular AR inhibitor, such as for example ARN-509, MDV3100, or RD162.In some embodiments, identification of such a mutation is used tocharacterize a subject as lacking responsiveness to an AR inhibitor thatis a CYP17A inhibitor, such as, for example galeterone (TOK001), TAK-700or abiraterone acetate.

Mutant AR Polypeptides

Provided herein are mutant AR polypeptides. In some embodiments, theisolated mutant AR polypeptides are isolated mutant AR polypeptides. Insome embodiments, the isolated mutant AR polypeptides are non-nativemutant AR polypeptides. In some embodiments, the isolated mutant ARpolypeptides are recombinant mutant AR polypeptides. In someembodiments, the mutant AR polypeptides provided herein exhibit androgenreceptor activity. For example, the mutant AR polypeptides bind toandrogen response elements and promote the expression of AR-responsivegenes. In some embodiments, the mutant AR polypeptides contain one ormore amino acid substitutions that confers resistance to full antagonismby an anti-androgen. In some embodiments, the mutant AR polypeptidescontain one or more amino acid substitutions that confers resistance tofull antagonism by a second-generation AR inhibitor, such as, but notlimited to, ARN-509, enzalutamide (MDV3100) or RD162. In someembodiments, the mutant AR polypeptides contain one or more amino acidsubstitutions that confers resistance to inhibition by ARN-509. In someembodiments, the mutant AR polypeptides contain one or more amino acidsubstitutions that confers resistance to inhibition by enzalutamide(MDV3100). In some embodiments, the mutant AR polypeptides contain oneor more amino acid substitutions that confers resistance to inhibitionby RD162.

In some embodiments, treatment of a mutant AR polypeptide providedherein with a second-generation AR inhibitor induces AR activity. Forexample, the second-generation AR inhibitor acts as an agonist of themutant AR polypeptide. In some embodiments, treatment of a mutant ARpolypeptide provided herein with ARN-509 induces AR activity. In someembodiments, treatment of a mutant AR polypeptide provided herein withenzalutamide (MDV3100) induces AR activity. In some embodiments,treatment of a mutant AR polypeptide provided herein with RD162 inducesAR activity.

In some embodiments, the mutant AR polypeptide comprises a modificationat a position corresponding to amino acid position 876 of the wild-typeAR polypeptide set forth in SEQ ID NO: 1 (Accession No. P10275) or acorresponding position in the wild-type AR polypeptide set forth in SEQID NO: 2 (Accession No. NP_000035.2). In some embodiments, themodification is a substitution of the amino acid phenylalanine at theposition corresponding to amino acid position 876 of the wild-type ARpolypeptide set forth in SEQ ID NO: 1. In some embodiments, the mutantandrogen receptor (AR) polypeptide does not comprise phenylalanine atthe position corresponding to amino acid position 876 of the wild-typeAR polypeptide set forth in SEQ ID NO: 1.

In some embodiments, the modification is a substitution of the aminoacid phenylalanine at the position corresponding to amino acid position876 of the wild-type AR polypeptide set forth in SEQ ID NO: 1, and thesubstituted amino acid is selected from among leucine, isoleucine,valine, alanine, glycine, methionine, serine, threonine, cysteine,tryptophan, lysine, arginine, histidine, proline, tyrosine, asparagine,glutamine, aspartic acid and glutamic acid. In some embodiments, themutant androgen receptor (AR) polypeptide comprises a leucine,isoleucine, valine, alanine, glycine, methionine, serine, threonine,cysteine, tryptophan, lysine, arginine, histidine, proline, tyrosine,asparagine, glutamine, aspartic acid or glutamic acid at the positioncorresponding to amino acid position 876 of the wild-type AR polypeptideset forth in SEQ ID NO: 1. In some embodiments, the modification is asubstitution of the amino acid phenylalanine at the positioncorresponding to amino acid position 876 of the wild-type AR polypeptideset forth in SEQ ID NO: 1, and the substituted amino acid is selectedfrom among leucine, isoleucine, valine, alanine, glycine, methionine andtryptophan. In some embodiments, the mutant androgen receptor (AR)polypeptide comprises a leucine, isoleucine, valine, alanine, glycine,methionine or tryptophan at the position corresponding to amino acidposition 876 of the wild-type AR polypeptide set forth in SEQ ID NO: 1.In some embodiments, the modification is a substitution of the aminoacid phenylalanine to leucine at the position corresponding to aminoacid position 876 of the wild-type AR polypeptide set forth in SEQ IDNO: 1. In some embodiments, the mutant AR polypeptide comprises aleucine at the position corresponding to amino acid position 876 of thewild-type AR polypeptide set forth in SEQ ID NO: 1.

In some embodiments, the modification comprises a deletion of the aminoacid phenylalanine at the position corresponding to amino acid position876 of the wild-type AR polypeptide set forth in SEQ ID NO: 1.

In some embodiments, the mutant AR polypeptide comprises a sequence ofamino acids set forth in SEQ ID NO: 5. In some embodiments the mutant ARpolypeptide comprises a polypeptide having a leucine at the positioncorresponding to amino acid position 876 and having 65%, 70%, 75%, 80%,85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity to thepolypeptide having the sequence set forth in SEQ ID NO: 5. In someembodiments the mutant AR polypeptide comprises a polypeptide not havinga phenylalanine at the position corresponding to amino acid position 876and having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%amino acid sequence identity to the polypeptide having the sequence setforth in SEQ ID NO: 5.

In some embodiments, the mutant AR polypeptide comprises a modificationat amino acid position 876 and a modification at one or more additionalamino acid positions. In some embodiments, the mutant AR polypeptidecomprises a modification at amino acid position 876 and a modificationat 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20or more amino acid positions. In some embodiments, the mutant ARpolypeptide comprises a modification at position 876 and a modificationat one additional amino acid position. In some embodiments, the mutantAR polypeptide comprises a leucine at amino acid position 876 and amodification at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20 or more additional amino acid positions. In someembodiments, the mutant AR polypeptide comprises a leucine at position876 and a modification at one additional amino acid position. In someembodiments, the modification at amino acid position 876 is asubstitution that is F876L.

In some embodiments, the mutant AR polypeptide comprises a modificationat position 876 and a modification at an additional amino acid positionthat confers resistance to a first- or second-generation AR antagonistor an AR antagonist that inhibits androgen production. In someembodiments, the modification at the amino acid position in addition tothe modification at amino acid 876 increases the resistance of the ARpolypeptide to a first- or second-generation AR antagonist or an ARantagonist that inhibits androgen production compared to an ARpolypeptide comprising the modification at amino acid position 876alone. In some embodiments, the modification at amino acid position 876is a substitution that is F876L.

In some embodiments, the mutant AR polypeptide comprises a modificationat position 876 and a modification selected from among AR modificationsdescribed in, for example. Grasso et al. (2012) Nature 487(7406):239-43;Ning et al. (2012) Urology 80(1):216-8; Cong et al. (2012) Gene500(2):220-3; Hay et al. (2012) PLoS One 2012; 7(3):e32514; Koochekpour(2010) Asian J Androl. 12(5):639-57; Waltering et al. (2012) Mol CellEndocrinol. 360:38-43; Robbins (2012) Mol Cell Endocrinol.352(1-2):26-33; or Gottlieb et al. (2012) Hum Mutat. 33(5):887-94. Insome embodiments, the modification at amino acid position 876 is asubstitution that is F876L.

In some embodiments, the mutant AR polypeptide comprises a modificationat position 876 and a modification selected from among AR modificationsassociated with castration resistant prostate cancer. In someembodiments, the modification associated with castration resistantprostate cancer is an amino acid substitution such as, for example,T877A, W741C, W741L, W741R. L701H or H874Y. In some embodiments, themodification at amino acid position 876 is a substitution that is F876L.

In some embodiments, the mutant AR polypeptide comprises a modificationat amino acid position 876 and a modification at amino acid position877. In some embodiments, the mutant AR polypeptide comprises a leucineat position 876 and a modification at amino acid position 877. In someembodiments, the modification at amino acid position 877 is asubstitution of the amino acid threonine. In some embodiments, thesubstituted amino acid at amino acid position 877 is selected from amongleucine, isoleucine, valine, alanine, phenylalanine, glycine,methionine, serine, cysteine, tryptophan, lysine, arginine, histidine,proline, tyrosine, asparagine, glutamine, aspartic acid and glutamicacid. In some embodiments, the substituted amino acid at amino acidposition 877 is alanine. In some embodiments, the mutant AR polypeptidecomprises a modification at position 876 and an alanine at amino acidposition 877. In some embodiments, the mutant AR polypeptide comprises aleucine at position 876 and an alanine at amino acid position 877.

In some embodiments, the mutant AR polypeptide comprises a modificationat position 876 and a modification at amino acid position 741. In someembodiments, the mutant AR polypeptide comprises a leucine at position876 and a modification at amino acid position 741. In some embodiments,the modification at amino acid position 741 is a substitution of theamino acid tryptophan. In some embodiments, the substituted amino acidat amino acid position 741 is selected from among leucine, isoleucine,valine, alanine, phenylalanine, glycine, methionine, serine, threonine,cysteine, lysine, arginine, histidine, proline, tyrosine, asparagine,glutamine, aspartic acid and glutamic acid. In some embodiments, thesubstituted amino acid at amino acid position 741 is leucine, cysteineor arginine. In some embodiments, the mutant AR polypeptide comprises amodification at position 876 and a leucine at amino acid position 741.In some embodiments, the mutant AR polypeptide comprises a modificationat position 876 and a cysteine at amino acid position 741. In someembodiments, the mutant AR polypeptide comprises a modification atposition 876 and an arginine at amino acid position 741. In someembodiments, the mutant AR polypeptide comprises a leucine at position876 and a leucine at amino acid position 741. In some embodiments, themutant AR polypeptide comprises a leucine at position 876 and a cysteineat amino acid position 741. In some embodiments, the mutant ARpolypeptide comprises a leucine at position 876 and an arginine at aminoacid position 741.

In some embodiments, the mutant AR polypeptide comprises a modificationat position 876 and a modification at amino acid position 701. In someembodiments, the mutant AR polypeptide comprises a leucine at position876 and a modification at amino acid position 701. In some embodiments,the modification at amino acid position 701 is a substitution of theamino acid leucine. In some embodiments, the substituted amino acid atamino acid position 701 is selected from among isoleucine, valine,alanine, phenylalanine, glycine, methionine, histidine, serine,threonine, cysteine, lysine, arginine, tryptophan, proline, tyrosine,asparagine, glutamine, aspartic acid and glutamic acid. In someembodiments, the substituted amino acid at amino acid position 701 ishistidine. In some embodiments, the mutant AR polypeptide comprises amodification at position 876 and a histidine at amino acid position 701.In some embodiments, the mutant AR polypeptide comprises a leucine atposition 876 and a histidine at amino acid position 701.

In some embodiments, the mutant AR polypeptide comprises a modificationat position 876 and a modification at amino acid position 874. In someembodiments, the mutant AR polypeptide comprises a leucine at position876 and a modification at amino acid position 874. In some embodiments,the modification at amino acid position 874 is a substitution of theamino acid histidine. In some embodiments, the substituted amino acid atamino acid position 874 is selected from among leucine, isoleucine,valine, alanine, phenylalanine, glycine, methionine, serine, threonine,cysteine, lysine, arginine, tryptophan, proline, tyrosine, asparagine,glutamine, aspartic acid and glutamic acid. In some embodiments, thesubstituted amino acid at amino acid position 874 is tyrosine. In someembodiments, the mutant AR polypeptide comprises a modification atposition 876 and a tyrosine at amino acid position 874. In someembodiments, the mutant AR polypeptide comprises a leucine at position876 and a tyrosine at amino acid position 874.

In some embodiments, the mutant AR polypeptide is an AR polypeptidevariant that comprises a modification at position 876 and one or moreadditional amino acid positions relative to the wild-type AR polypeptideset forth in SEQ ID NO: 1. Exemplary variants include, for example,species variants, allelic variants. RNA splicing variants and variantsthat contain conservative and non-conservative amino acid mutations. Insome embodiments, the AR polypeptide variant comprises a polyglutaminetract of about 6 consecutive glutamine residues to about 39 consecutiveglutamine residues. In some embodiments, the AR polypeptide variantcomprises a polyglutamine tract of about 16 consecutive glutamineresidues to about 29 consecutive glutamine residues. In someembodiments, the AR polypeptide variant comprises a polyglutamine tractof about 21 consecutive glutamine residues. In some embodiments, the ARpolypeptide variant comprises a polyglutamine tract of about 22consecutive glutamine residues. In some embodiments, the AR polypeptidevariant comprises a polyglutamine tract of about 23 consecutiveglutamine residues. In some embodiments, the AR polypeptide variantcomprises a polyglycine tract of about 10 consecutive glycine residuesto about 27 consecutive glycine residues. In some embodiments, the ARpolypeptide variant comprises a polyglycine tract of about 23consecutive glycine residues. In some embodiments, the AR polypeptidevariant comprises a polyglycine tract of about 24 consecutive glycineresidues.

In some embodiments, the mutant AR polypeptide comprises a portion ofthe mutant AR polypeptide set forth in SEQ ID NO: 5. In someembodiments, the portion exhibits an activity of an AR polypeptide. Insome embodiments, the mutant AR polypeptide comprises the DNA bindingdomain of an AR polypeptide and the ligand binding domain of the ARpolypeptide comprising the modification at amino acid position 876 ofthe mutant AR polypeptide set forth in SEQ ID NO: 5. In someembodiments, the mutant AR polypeptide consists essentially of the DNAbinding domain of an AR polypeptide and the ligand binding domain of theAR polypeptide comprising the modification at amino acid position 876 ofthe mutant AR polypeptide set forth in SEQ ID NO: 5. In someembodiments, the mutant AR polypeptide comprises the sequence of aminoacids from about amino acid position 554 to about amino acid position919 of the mutant AR polypeptide set forth in SEQ ID NO: 5. In someembodiments, the mutant AR polypeptide comprises the ligand bindingdomain of the mutant AR polypeptide. In some embodiments, the mutant ARpolypeptide consists essentially of the ligand binding domain of themutant AR polypeptide. In some embodiments, the mutant AR polypeptidecomprises the sequence of amino acids from about amino acid position 554to about amino acid position 919.

In some embodiments, an AR polypeptide is a fusion protein comprisingthe ligand binding domain of an AR polypeptide comprising themodification at amino acid position 876 of the wild-type AR polypeptideset forth in SEQ ID NO: 1 linked to a heterologous polypeptide. In someembodiments, the modification is an amino acid substitution that isF876L. Methods for the generation of fusion proteins are known in theart and include standard recombinant DNA techniques. For example, insome embodiments, DNA fragments coding for the different polypeptidesequences are ligated together in-frame in accordance with conventionaltechniques, for example by employing blunt-ended or stagger-endedtermini for ligation, restriction enzyme digestion to provide forappropriate termini, filling-in of cohesive ends as appropriate,alkaline phosphatase treatment to avoid undesirable joining, andenzymatic ligation. In some embodiments, the fusion gene can besynthesized by conventional techniques including automated DNAsynthesizers. In some embodiments, PCR amplification of gene fragmentscan be carried out using anchor primers which give rise to complementaryoverhangs between two consecutive gene fragments which can subsequentlybe annealed and reamplified to generate a chimeric gene sequence (see,for example. Current Protocols in Molecular Biology, eds. Ausubel et al.John Wiley & Sons: 1992). In some embodiments, expression vectors arecommercially available that encode a fusion moiety (e.g., a GSTpolypeptide). A nucleic acid encoding a modified AR polypeptide can becloned into such an expression vector such that the fusion moiety islinked in-frame to the modified AR polypeptide.

In some embodiments, an AR polypeptide is a fusion protein comprisingthe ligand binding domain of an AR polypeptide comprising a modificationat amino acid position 876 of the wild-type AR polypeptide set forth inSEQ ID NO: 1 linked to a heterologous DNA binding domain. In someembodiments, an AR polypeptide is a fusion protein comprising the ligandbinding domain of a mutant AR polypeptide set forth in SEQ ID NO: 5linked to a heterologous DNA binding domain. In some embodiments theheterologous DNA binding domain is GAL4 DNA binding domain. In someembodiments the heterologous DNA binding domain is LexA DNA bindingdomain. In some embodiments, the ligand binding domain of an ARpolypeptide comprising a modification at amino acid position 876 of thewild-type AR polypeptide set forth in SEQ ID NO: 1 linked to aheterologous DNA binding domain via a peptide linker. In someembodiments, an AR polypeptide is a fusion protein comprising the ligandbinding domain of a mutant AR polypeptide set forth in SEQ ID NO: 5linked to a heterologous DNA binding domain via a peptide linker.

In some embodiments, an AR polypeptide is a fusion protein comprisingthe ligand binding domain of an AR polypeptide comprising a modificationat amino acid position 876 of the wild-type AR polypeptide set forth inSEQ ID NO: 1 linked to a heterologous peptide for use in an proteininteraction assay, such as, but not limited to a yeast two hybrid assay,a mammalian cell based two hybrid (M2H) system, a Förster (Fluorescence)Resonance Energy Transfer (FRET) assay, a Bioluminescence ResonanceEnergy Transfer (BRET), or a Homogeneous Time Resolved Fluorescence(HTRF®) assay. In some embodiments, an AR polypeptide is a fusionprotein comprising the ligand binding domain of a mutant AR polypeptideset forth in SEQ ID NO: 5 linked to a heterologous peptide for use in anprotein interaction assay, such as, but not limited to a yeast twohybrid assay, a mammalian cell based two hybrid (M2H) system, a Förster(Fluorescence) Resonance Energy Transfer (FRET) assay, a BioluminescenceResonance Energy Transfer (BRET), or a Homogeneous Time ResolvedFluorescence (HTRF®) assay.

In some embodiments, the ligand binding domain of an AR polypeptidecomprising a modification at amino acid position 876 of the wild-type ARpolypeptide set forth in SEQ ID NO: 1 linked to a detectablepolypeptide. In some embodiments, the ligand binding domain of a mutantAR polypeptide set forth in SEQ ID NO: 5 is linked to a detectablepolypeptide. In some embodiments, the ligand binding domain of an ARpolypeptide comprising a modification at amino acid position 876 of thewild-type AR polypeptide set forth in SEQ ID NO: 1 linked to afluorescent protein, such as, but limited to, a green (GFP), red (RFP),cyan (CFP), yellow (YFP), or blue (BFP) fluorescent protein. In someembodiments, the ligand binding domain of a mutant AR polypeptide setforth in SEQ ID NO: 5 is linked to a fluorescent protein, such as, butlimited to, a green (GFP), red (RFP), cyan (CFP), yellow (YFP), or blue(BFP) fluorescent protein. In some embodiments, the ligand bindingdomain of an AR polypeptide comprising a modification at amino acidposition 876 of the wild-type AR polypeptide set forth in SEQ ID NO: 1linked to a bioluminescent protein. In some embodiments, the ligandbinding domain of a mutant AR polypeptide set forth in SEQ ID NO: 5 islinked to a bioluminescent protein. In some embodiments, the ligandbinding domain of an AR polypeptide comprising a modification at aminoacid position 876 of the wild-type AR polypeptide set forth in SEQ IDNO: 1 linked to a peptide tag. In some embodiments, the ligand bindingdomain of a mutant AR polypeptide set forth in SEQ ID NO: 5 is linked toa peptide tag. In some embodiments, the peptide tag is an epitope tagrecognized by a tag-specific antibody. In some embodiments the tag is anepitope tag, such as, but not limited to a c-myc, V-5, hemagglutinin(HA), FLAG. In some embodiments the tag is an affinity tag, such as, butnot limited to, biotin, strep-tag, chitin binding protein (CBP), maltosebinding protein (MBP), glutathione-S-transferase (GST), or a poly(His)tag.

In some embodiments, provided herein is an array comprising a mutant ARpolypeptide provided herein. In some embodiments, the mutant ARpolypeptide is bound to a microchip. In some embodiments, the mutant ARpolypeptide is bound directly to the microchip. In some embodiments, themutant AR polypeptide is bound indirectly to the microchip via a linker.In some embodiments, provided herein is a microchip array comprising amutant AR polypeptide provided herein.

Nucleic Acids

Provided herein are nucleic acids encoding mutant AR polypeptides.Provided herein are nucleic acids encoding any of the mutant ARpolypeptides described herein. Methods for deducing nucleic acids thatencode particular polypeptides are known in the art and involve standardmolecular biology techniques. Exemplary nucleic acids encoding mutant ARpolypeptides provided herein are provided. It is understood that due tothe degeneracy of the genetic code multiple variants nucleic acids existthat encode the same polypeptide. Nucleic acids that encode the mutantAR polypeptides provided herein encompass such variants. In someembodiments, the mutant AR nucleic acids are synthetic nucleic acids. Insome embodiments, the mutant AR nucleic acids are cDNA molecules. Insome embodiments, the mutant AR nucleic acids do not contain genomicDNA. In some embodiments, the mutant AR nucleic acids are unmethylated.In some embodiments, the mutant AR nucleic acids are do not contain ARgenomic intron sequences. In some embodiments, the mutant AR nucleicacids comprise a sequence of nucleotides from two or more exons of theAR genomic sequence, including exon 8 or a portion thereof comprisingthe nucleic acid sequence encoding position 876 of the AR polypeptide.In some embodiments, the mutant AR nucleic acids comprise a sequence ofnucleotides that encode phenylalanine at a position corresponding toposition 876 of the wild-type AR polypeptide.

In some embodiments, the nucleic acid encoding mutant AR polypeptidescomprises a modification relative to a nucleic acid encoding a wild-typeAR polypeptide. In some embodiments, the nucleic acid encoding a mutantAR polypeptide comprises a modification where the encoded polypeptidecomprises a substitution of the amino acid phenylalanine at the positioncorresponding to amino acid position 876 of the wild-type AR polypeptideset forth in SEQ ID NO: 1. In some embodiments, the nucleic acidencoding a mutant AR polypeptide comprises a modification where encodedpolypeptide does not comprise phenylalanine at the positioncorresponding to amino acid position 876 of the wild-type AR polypeptideset forth in SEQ ID NO: 1.

In some embodiments the nucleic acid modification is a missense mutationor a deletion of one or more codons that encode the polypeptide. In someembodiments, the modification is a missense mutation that changes thenucleic acid codon that encodes phenylalanine at amino position 876 ofthe AR polypeptide. In some embodiments, the nucleic acid codon thatencodes phenylalanine at amino position 876 of the AR polypeptide is TTCor TTT. In some embodiments, the nucleic acid codon that encodesphenylalanine at amino position 876 of the AR polypeptide is TTC. Insome embodiments, the nucleic acid codon that encodes phenylalanine atamino position 876 of the AR polypeptide is TIT. In some embodiments,the modification changes the nucleic acid codon that encodesphenylalanine at amino position 876 of the AR polypeptide from TTC to anucleic acid codon that encodes leucine. In some embodiments, themodification changes the nucleic acid codon that encodes phenylalanineat amino position 876 of the AR polypeptide from TIT to a nucleic acidcodon that encodes leucine. In some embodiments, the nucleic acid codonthat encodes leucine is selected from among TTA, TTG, CTT, CTC, CTA orCTG.

In some embodiments, the modification is a missense mutation thatcomprises a substitution of Thymine (T) for Cytosine (C). In someembodiments, the modification changes the nucleic acid codon thatencodes phenylalanine at amino position 876 of the AR polypeptide fromTTC to CTC. In some embodiments, the modification is a missense mutationthat comprises a substitution of Thymine (T) for Cytosine (C) at nucleicacid position 2626 of the AR nucleic acid sequence set forth in SEQ IDNO: 18.

In some embodiments, the modification is a missense mutation thatcomprises a substitution of Thymine (T) for Adenine (A). In someembodiments, the modification changes the nucleic acid codon thatencodes phenylalanine at amino position 876 of the AR polypeptide fromTTT to TTA. In some embodiments, the modification is a missense mutationthat comprises a substitution of Thymine (T) for Adenine (A) at nucleicacid position 2628 of the AR nucleic acid sequence set forth in SEQ IDNO: 18.

In some embodiments, the modification is a missense mutation thatcomprises a substitution of Thymine (T) for Guanine (G). In someembodiments, the modification changes the nucleic acid codon thatencodes phenylalanine at amino position 876 of the AR polypeptide fromTTT to TTG. In some embodiments, the modification is a missense mutationthat comprises a substitution of Thymine (T) for Guanine (G) at nucleicacid position 2628 of the AR nucleic acid sequence set forth in SEQ IDNO: 18.

In some embodiments, the modification comprises a missense mutation thatcomprises a substitution of Thymine (T) for Cytosine (C) at the firstposition of the codon that encodes F876 of the AR polypeptide and asecond missense mutation that comprises a substitution of Thymine (T)for Adenosine (A) at the third position of the codon that encodes F876of the AR polypeptide. In some embodiments, the modification changes thenucleic acid codon that encodes phenylalanine at amino position 876 ofthe AR polypeptide from TTT to CTA. In some embodiments, themodification is a missense mutation that comprises a substitution ofThymine (T) for Cytosine (C) at nucleic acid position 2626 and a secondmissense mutation that comprises a substitution of Thymine (T) forAdenosine (A) at nucleic acid position 2628 of the AR nucleic acidsequence set forth in SEQ ID NO: 18.

In some embodiments, the modification comprises a missense mutation thatcomprises a substitution of Thymine (T) for Cytosine (C) at the firstposition of the codon that encodes F876 of the AR polypeptide and asecond missense mutation that comprises a substitution of Thymine (T)for Guanine (G) at the third position of the codon that encodes F876 ofthe AR polypeptide. In some embodiments, the modification changes thenucleic acid codon that encodes phenylalanine at amino position 876 ofthe AR polypeptide from TTT to CTG. In some embodiments, themodification is a missense mutation that comprises a substitution ofThymine (T) for Cytosine (C) at nucleic acid position 2626 and a secondmissense mutation that comprises a substitution of Thymine (T) forGuanine (G) at nucleic acid position 2628 of the AR nucleic acidsequence set forth in SEQ ID NO: 18.

In some embodiments the nucleic acid encoding the mutant AR polypeptidecomprises a sequence of nucleotides set forth in SEQ ID NO: 19. In someembodiments the nucleic acid encoding the mutant AR polypeptidecomprises a nucleic acid having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%,97%, 98%, or 99% nucleotide acid sequence identity to the nucleic acidhaving the sequence of nucleotides set forth in SEQ ID NO: 19, where theencoded mutant AR comprises a modification relative to the wild-type ARpolypeptide at a position corresponding to amino acid position 876. Insome embodiments the nucleic acid encoding the mutant AR polypeptidecomprises a nucleic acid having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%,97/%, 98%, or 99% nucleotide acid sequence identity to the nucleic acidhaving the sequence of nucleotides set forth in SEQ ID NO: 19, where theencoded mutant AR does not comprise a phenylalanine at the positioncorresponding to amino acid position 876. In some embodiments thenucleic acid encoding the mutant AR polypeptide comprises a nucleic acidhaving 650/%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%nucleotide acid sequence identity to the nucleic acid having thesequence of nucleotides set forth in SEQ ID NO: 19, where the encodedmutant AR comprises a leucine at the position corresponding to aminoacid position 876.

In some embodiments, the nucleic acid provided herein encoding a mutantAR polypeptide is an isolated nucleic acid. In some embodiments, thenucleic acid provided herein encoding a mutant AR polypeptide is a DNAmolecule. In some embodiments, the nucleic acid provided herein encodinga mutant AR polypeptide is a cDNA molecule. In some embodiments, thenucleic acid provided herein encoding a mutant AR polypeptide is an RNAmolecule. In some embodiments, the nucleic acid provided herein encodinga mutant AR polypeptide is an inhibitory RNA molecule (i.e. RNAi). Insome embodiments, the nucleic acid provided herein is a nucleic acidmolecule that is complementary, or binds to, an nucleic acid encoding amutant AR polypeptide.

In some embodiments, the nucleic acid provided herein encoding a mutantAR polypeptide or a portion thereof contains nucleic acid encoding anamino acid at position 876 that is not phenylalanine. In someembodiments, the nucleic acid provided herein encoding a mutant ARpolypeptide or a portion thereof contains nucleic acid encoding leucineat amino acid position 876.

In some embodiments, the nucleic acid provide herein is anoligonucleotide that encodes a portion of the mutant AR polypeptide. Insome embodiments the nucleic acid provided herein is an oligonucleotidethat encodes a portion of the mutant AR polypeptide that contains anucleotide codon encoding the amino acid corresponding to amino acidposition 876. In some embodiments, the codon encodes an amino acid thatis not phenylalanine. In some embodiments, the codon encodes an aminoacid that is leucine.

In some embodiments, the nucleic acid provided herein is a vector thatcomprises nucleic acid encoding any of the mutant AR polypeptidesprovided herein. In some embodiments, the nucleic acid provided hereinis a vector that comprises nucleic acid encoding any of the mutant ARpolypeptides provided herein is an expression vector. In someembodiments, the nucleic acid provided herein is a vector that comprisesnucleic acid encoding any of the mutant AR polypeptides provided hereinis operably linked to a promoter for the expression of the mutant ARpolypeptides.

In some embodiments, the vector is a plasmid vector. In someembodiments, the vector is a viral vector. In some embodiments, theviral vector is a DNA or RNA viral vector. Exemplary viral vectorsinclude, but are not limited to, a vaccinia, adenovirus,adeno-associated virus (AAV), retrovirus, or herpesvirus vector.

In some embodiments, provided herein is an array comprising a nucleicacid encoding any of the mutant AR polypeptides provided herein. In someembodiments, the mutant AR nucleic acid is bound to a microchip. In someembodiments, the mutant AR nucleic acid is bound directly to themicrochip. In some embodiments, the mutant AR nucleic acid is boundindirectly to the microchip via a linker. In some embodiments, providedherein is a microchip array comprising a nucleic acid encoding any ofthe mutant AR polypeptides provided herein.

Production of Nucleic Acids and Polypeptides

In some embodiments, an isolated nucleic acid molecule encoding a mutantAR polypeptide provided herein is generated by standard recombinantmethods. In some embodiments, an isolated nucleic acid molecule encodinga mutant AR polypeptide provided herein is generated by amplification ofa mutant AR sequence from genomic DNA. In some embodiments, an isolatednucleic acid molecule encoding a mutant AR polypeptide provided hereinis generated by polymerase chain reaction using AR sequence specificprimers. In some embodiments, an isolated nucleic acid molecule encodinga mutant AR polypeptide provided herein is generated by reversetranscription of mRNA encoding a mutant AR polypeptide.

In some embodiments, an isolated nucleic acid molecule encoding a mutantAR polypeptide provided herein is inserted into an expression vector andexpressed in a host cell or a non-cell extract. In some embodiments, anisolated nucleic acid molecule encoding a mutant AR polypeptide providedherein is operatively linked to a promoter for expression of theencoding polypeptide in a cell or non-cell extract. In some embodiments,the promoter is a constitutive promoter. In some embodiments, thepromoter is an inducible promoter.

In some embodiments, the nucleic acid molecule encoding a mutant ARpolypeptide provided herein is “exogenous” to a cell, which means thatit is foreign to the cell into which the vector is being introduced orthat the sequence is homologous to a sequence in the cell but in aposition within the host cell nucleic acid in which the sequence isordinarily not found. Vectors include plasmids, cosmids, viruses(bacteriophage, animal viruses, and plant viruses), and artificialchromosomes (e.g., YACs). One of skill in the art would be well equippedto construct a vector through standard recombinant techniques, which aredescribed in Sambrook et al., 1989 and Ausubel et al., 1996, bothincorporated herein by reference.

Methods for the expression of a protein in a cell are well known in theart and include, for example, expression in cells, such as animal andplant cells. Exemplary animal cells for the expression of mutant ARpolypeptides provided herein include but are not limited to bacteria,yeast, insect cells, and mammalian cells, such as for example, human,primate, rodent, bovine, and ovine cells. In some embodiments, thenucleic acid encoding the mutant AR is integrated into the genome of thehost cell.

In some embodiments, a method for the expression of a mutant ARpolypeptide provided herein comprises culturing a host cell containingan expression vector encoding a mutant AR polypeptide such that themutant AR polypeptide is produced by the cell. In some methods, thenucleic acid encoding the mutant polypeptide is connected to nucleicacid encoding a signal sequence such that the signal sequence isexpressed as a fusion peptide with the mutant AR polypeptide. In someembodiments the signal sequence allows for the secretion of the mutantAR polypeptide by the host cell.

In some embodiments the mutant AR polypeptide is isolated from a hostcell expressing the mutant polypeptide. In some embodiments an extractis prepared from the host cell and the mutant AR polypeptide is isolatedby purification methods such as but not limited to chromatography orimmunoaffinity with an antibody that is specific for AR polypeptides orspecific to the mutant AR polypeptide in particular.

Antibodies

In some embodiments the antibody binds to a mutant AR polypeptideprovided herein, and binds with less affinity or does not bind to awild-type AR polypeptide. In some embodiments the antibody binds to amutant AR polypeptide in the presence of a second-generation inhibitor,such as, but not limited to ARN-509, enzalutamide (MDV3100) or RD162.

In some embodiments, mutant AR polypeptide provided herein are detectedusing antibodies that specifically recognize the mutant AR polypeptides,but do not recognize wild-type AR polypeptides. In some embodiments,mutant AR polypeptide provided herein are detected using antibodies thatspecifically recognize a mutant AR polypeptide having a leucine at aminoacid position 876, but do not recognize wild-type AR polypeptides. Insome embodiments, antibodies are raised against one or more allelicforms of the mutant AR polypeptide provided herein. Techniques for usinga specific protein or an oligopeptide as an antigen to elicit antibodiesthat specifically recognize epitopes on the peptide or protein are wellknown. In one embodiment, the DNA sequence of the desired allelic formof the target gene is cloned by insertion into an appropriate expressionvector and translated into protein in a prokaryotic or eukaryotic hostcell. The protein can be recovered and used as an antigen to elicit theproduction of specific antibodies. In another embodiment, the DNA of thedesired allelic form of the target gene is amplified by PCR technologyand is subsequently translated in vitro into protein to be used as theantigen to elicit the production of specific antibodies. In anotherembodiment, the DNA sequence of the alternative alleles is used as abasis for the generation of synthetic peptides representing the aminoacid sequence of the alleles for use as the antigen to elicit theproduction of specific antibodies.

In some embodiments, antibodies are generated either by standardmonoclonal antibody techniques or generated through recombinant basedexpression systems. See generally, Abbas, Lichtman, and Pober, Cellularand Molecular Immunology, W. B. Saunders Co. (1991). The term“antibodies” is meant to include intact antibody molecules as well asantibody fragments or derivatives, such as Fab and F(ab′)2, which arecapable of specifically binding to antigen. The antibodies so producedpreferentially bind only the mutant protein produced in the allelic formwhich was used as an antigen to create the antibody. Methods ofgenerating allele-specific antibodies are also described in U.S. Pat.No. 6,200,754 and U.S. Pat. No. 6,054,273, the entire contents of whichare incorporated herein by reference.

In some embodiments, the antibody provided herein is a humanizedantibody. A “humanized antibody” refers to a type of engineered antibodyhaving its CDRs derived from a non-human donor immunoglobulin, theremaining immunoglobulin-derived parts of the molecule being derivedfrom one or more human immunoglobulin(s). In some embodiments, frameworksupport residues are altered to preserve binding affinity (see, e.g.,Queen et al. Proc. Natl. Acad Sci USA, 86:10029-10032 (1989), Hodgson etal. Bio/Technology. 9:421 (1991)). In some embodiments, a suitable humanacceptor antibody is one selected from a conventional database, e.g.,the KABAT® database, Los Alamos database, and Swiss Protein database, byhomology to the nucleotide and amino acid sequences of the donorantibody. In some embodiments, a human antibody characterized by ahomology to the framework regions of the donor antibody (on an aminoacid basis) is suitable to provide a heavy chain constant region and/ora heavy chain variable framework region for insertion of the donor CDRs.In some embodiments, a suitable acceptor antibody capable of donatinglight chain constant or variable framework regions is selected in asimilar manner. In some embodiments, the acceptor antibody heavy andlight chains originate from the same acceptor antibody. In someembodiments, the acceptor antibody heavy and light chains originate fromthe different acceptor antibodies. The prior art describes several waysof producing such humanized antibodies-see, for example, EP-A-0239400and EP-A-054951.

In some embodiments, antibodies specific for mutant AR polypeptideprovided herein can be used to detect the presence of a mutant ARpolypeptide provided herein in a sample, e.g., an assay sample, a cellsample, a cell extract, a biological sample, or a patient sample, usingtechniques known in the art. These techniques include, for example,Western blot, immunohistochemistry, indirect immunofluorescence, andantibody microarray. In some embodiments, antibodies which specificallyrecognize mutant AR polypeptide are third-generation AR inhibitors. Insome embodiments, the ability of an antibody which specificallyrecognizes a mutant AR polypeptide to inhibit the biological activity ofthe mutant AR polypeptide can be determined using the methods describedherein for identifying third-generation AR inhibitors.

Diagnostic Assays for Detecting Mutant AR Polypeptides and Nucleic AcidsEncoding Mutant AR Polypeptides

Provided herein are diagnostic methods that involve the detection of amutant AR polypeptide in a subject or a nucleic acid encoding a mutantAR polypeptide in a subject. In some embodiments, the subject has anAR-mediated disease or condition. In some embodiments, the diagnosticmethods are employed for the screening subjects having a cancer that isresistant to therapy with an anti-androgen, such as a first- orsecond-generation AR antagonist, identifying subjects for the treatmentwith anti-androgen, such as a first- or second-generation AR antagonist,monitoring the therapy of subjects receiving an anti-androgen therapy,such as a first- or second-generation AR antagonist, optimizing thetherapy of subjects receiving an anti-androgen therapy, such as a first-or second-generation AR antagonist, and combinations thereof. In someembodiments, the methods comprises selecting a subject for therapy witha third-generation AR antagonist. In some embodiments, the methodsfurther comprise administering to the subject a third-generation ARantagonist as described herein. In some embodiments, the mutant ARpolypeptide detected comprises a modification at a positioncorresponding to amino acid position 876 of the wild-type AR polypeptideset forth in SEQ ID NO: 1. In some embodiments, the mutant ARpolypeptide detected comprises a substitution of the amino acidphenylalanine to leucine at the position corresponding to amino acidposition 876 of the wild-type AR polypeptide set forth in SEQ ID NO: 1.In some embodiments, a subject having a mutant AR polypeptide comprisinga modification at amino acid position 876 is resistant to inhibitionwith a first- or a second-generation antagonist.

In some embodiments, a subject having a mutant AR polypeptide comprisinga modification at amino acid position 876 is resistant to inhibitionwith a first- or a second-generation antagonist. In some embodiments, asubject having a mutant AR polypeptide comprising a modification atamino acid position 876 is resistant to inhibition with a first- and asecond-generation antagonist. In some embodiments, a subject having amutant AR polypeptide comprising a leucine at amino acid position 876 isresistant to inhibition with a first- or a second-generation antagonist.In some embodiments, a subject having a mutant AR polypeptide comprisinga leucine at amino acid position 876 is resistant to inhibition with afirst- and a second-generation antagonist. In some embodiments, asubject having a mutant AR polypeptide comprising a modification atamino acid position 876 is resistant to inhibition with a CYP17Ainhibitor that binds to AR, such as for example, galeterone (TOK001).TAK-700 or abiraterone acetate. In some embodiments, a subject having amutant AR polypeptide comprising a modification at amino acid position876 is resistant to inhibition with a CYP17A inhibitor that binds to AR,such as for example, galeterone (TOK001), TAK-700 or abirateroneacetate.

In some embodiments, provided are methods for characterizing an ARpolypeptide that is resistant to inhibition with a second-generation ARantagonist in a subject, comprising: (a) assaying a sample containing anucleic acid molecule encoding an AR polypeptide from the subject todetermine whether the encoded AR polypeptide is modified at an aminoacid position corresponding to amino acid position 876 of the amino acidsequence set forth in SEQ ID NO: 1; and (b) characterizing the AR asresistant to inhibition with a second-generation AR antagonist if thesubject has the modification. In some embodiments, the method furthercomprises administration of a third-generation AR antagonist providedherein for inhibition of the mutant AR. In some embodiments, the methodfurther comprises not administering a second generation AR antagonist.In some embodiments, the method further comprises administering a secondgeneration AR antagonist if the subject does not have the modification.In some embodiments, the subject has cancer. In some embodiments, thesubject has a prostate cancer. In some embodiments, the subject has acastration resistant prostate cancer. In some embodiments, the methodfurther comprises a step of obtaining the nucleic acid sample from thesubject.

In some embodiments, provided are methods for characterizing an AR thatis resistant to inhibition with a first-generation AR antagonist in asubject, comprising: (a) assaying a sample containing a nucleic acidmolecule encoding an AR polypeptide from the subject to determinewhether the encoded AR polypeptide is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; and (b) characterizing the AR as resistant toinhibition with a first-generation AR antagonist if the subject has themodification. In some embodiments, the method further comprisesadministration of a third-generation AR antagonist provided herein forinhibition of the mutant AR. In some embodiments, the method furthercomprises not administering a second generation AR antagonist. In someembodiments, the method further comprises administering a secondgeneration AR antagonist if the subject does not have the modification.In some embodiments, the subject has cancer. In some embodiments, thesubject has a prostate cancer. In some embodiments, the subject has acastration resistant prostate cancer. In some embodiments, the methodfurther comprises obtaining the nucleic acid sample from the subject.

In some embodiments, provided are methods for charactering an AR that isresistant to inhibition with an AR antagonist that is a CYP17A inhibitorin a subject, comprising: (a) assaying a sample containing a nucleicacid molecule encoding an AR polypeptide from the subject to determinewhether the encoded AR polypeptide is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; and (b) characterizing the AR as resistant toinhibition with an AR antagonist that is a CYP17A inhibitor if thesubject has the modification. In some embodiments, the method furthercomprises administration of a third-generation AR antagonist providedherein for inhibition of the mutant AR. In some embodiments, the methodfurther comprises not administering a second generation AR antagonist.In some embodiments, the method further comprises administering a secondgeneration AR antagonist if the subject does not have the modification.In some embodiments, the subject has cancer. In some embodiments, thesubject has a prostate cancer. In some embodiments, the subject has acastration resistant prostate cancer. In some embodiments the CYP17Ainhibitor is galeterone (TOK001). TAK-700 or abiraterone acetate. Insome embodiments, the method further comprises obtaining the nucleicacid sample from the subject.

In some embodiments, provided are methods for selecting a subject fortherapy with a second-generation AR antagonist, comprising (a) assayinga sample containing a nucleic acid molecule encoding an AR polypeptidefrom the subject to determine whether the encoded AR polypeptide ismodified at an amino acid position corresponding to amino acid position876 of the amino acid sequence set forth in SEQ ID NO: 1; and (b)characterizing the subject as a candidate for therapy with asecond-generation AR antagonist if the subject does not have themodification. In some embodiments, the method further comprisescharacterizing the subject as not a candidate for therapy with asecond-generation AR antagonist if the subject has the modification. Insome embodiments, the method further comprises administration of athird-generation AR antagonist provided herein for inhibition of themutant AR. In some embodiments, the subject has cancer. In someembodiments, the subject has a prostate cancer. In some embodiments, thesubject has a castration resistant prostate cancer. In some embodiments,the method further comprises a step of obtaining the nucleic acid samplefrom the subject.

In some embodiments, provided are methods for selecting a subject fortherapy with a first-generation AR antagonist, comprising (a) assaying asample containing a nucleic acid molecule encoding an AR polypeptidefrom the subject to determine whether the encoded AR polypeptide ismodified at an amino acid position corresponding to amino acid position876 of the amino acid sequence set forth in SEQ ID NO: 1; and (b)characterizing the subject as a candidate for therapy with afirst-generation AR antagonist if the subject does not have themodification. In some embodiments, the method further comprisescharacterizing the subject as not a candidate for therapy with afirst-generation AR antagonist if the subject has the modification. Insome embodiments, the method further comprises administration of athird-generation AR antagonist provided herein for inhibition of themutant AR. In some embodiments, the subject has cancer. In someembodiments, the subject has a prostate cancer. In some embodiments, thesubject has a castration resistant prostate cancer. In some embodiments,the method further comprises a step of obtaining the nucleic acid samplefrom the subject.

In some embodiments, provided are methods for selecting a subject fortherapy with an AR antagonist that is a CYP17A inhibitor, comprising (a)assaying a sample containing a nucleic acid molecule encoding an ARpolypeptide from the subject to determine whether the encoded ARpolypeptide is modified at an amino acid position corresponding to aminoacid position 876 of the amino acid sequence set forth in SEQ ID NO: 1;and (b) characterizing the subject as a candidate for therapy with an ARantagonist that is a CYP17A inhibitor if the subject does not have themodification. In some embodiments, the method further comprisescharacterizing the subject as not a candidate for therapy with a CYP17Ainhibitor if the subject has the modification. In some embodiments, themethod further comprises administration of a third-generation ARantagonist provided herein for inhibition of the mutant AR. In someembodiments, the subject has cancer. In some embodiments, the subjecthas a prostate cancer. In some embodiments, the subject has a castrationresistant prostate cancer. In some embodiments the CYP17A inhibitor isgaleterone (TOK001), TAK-700 or abiraterone acetate. In someembodiments, the method further comprises a step of obtaining thenucleic acid sample from the subject.

In some embodiments, provided are methods for selecting a subject fortherapy with a third-generation AR antagonist, comprising (a) assaying asample containing a nucleic acid molecule encoding an AR polypeptidefrom the subject to determine whether the encoded AR polypeptide ismodified at an amino acid position corresponding to amino acid position876 of the amino acid sequence set forth in SEQ ID NO: 1; and (b)characterizing the subject as a candidate for therapy with athird-generation AR antagonist if the subject has the modification. Insome embodiments, the method further comprises administration of athird-generation AR antagonist provided herein for inhibition of themutant AR. In some embodiments, the subject has cancer. In someembodiments, the subject has a prostate cancer. In some embodiments, thesubject has a castration resistant prostate cancer. In some embodiments,the method further comprises a step of obtaining the nucleic acid samplefrom the subject.

In some embodiments, provided are methods for determining whether asubject is or is likely to become resistant to therapy with asecond-generation AR antagonist, comprising: (a) assaying a samplecontaining a nucleic acid molecule encoding an AR polypeptide from thesubject to determine whether the encoded AR polypeptide is modified atan amino acid position corresponding to amino acid position 876 of theamino acid sequence set forth in SEQ ID NO: 1; and (b) characterizingthe subject as resistant or is likely to become resistant to therapywith a second-generation AR antagonist if the subject has themodification. In some embodiments, the method further comprisesadministration of a third-generation AR inhibitor provided herein forinhibition of the mutant AR. In some embodiments, the subject hascancer. In some embodiments, the subject has a prostate cancer. In someembodiments, the subject has a castration resistant prostate cancer. Insome embodiments, the method further comprises a step of obtaining thenucleic acid sample from the subject.

In some embodiments, provided are methods for determining whether asubject is or is likely to become resistant to therapy with afirst-generation AR antagonist, comprising: (a) assaying a samplecontaining a nucleic acid molecule encoding an AR polypeptide from thesubject to determine whether the encoded AR polypeptide is modified atan amino acid position corresponding to amino acid position 876 of theamino acid sequence set forth in SEQ ID NO: 1; and (b) characterizingthe subject as resistant or is likely to become resistant to therapywith a first-generation AR antagonist if the subject has themodification. In some embodiments, the method further comprisesadministration of a third-generation AR inhibitor provided herein forinhibition of the mutant AR. In some embodiments, the subject hascancer. In some embodiments, the subject has a prostate cancer. In someembodiments, the subject has a castration resistant prostate cancer. Insome embodiments, the method further comprises a step of obtaining thenucleic acid sample from the subject.

In some embodiments, provided are methods for determining whether asubject is or is likely to become resistant to therapy with an ARantagonist that is a CYP17A inhibitor, comprising: (a) assaying a samplecontaining a nucleic acid molecule encoding an AR polypeptide from thesubject to determine whether the encoded AR polypeptide is modified atan amino acid position corresponding to amino acid position 876 of theamino acid sequence set forth in SEQ ID NO: 1 and (b) characterizing thesubject as resistant or is likely to become resistant to therapy with anAR antagonist that is a CYP17A inhibitor if the subject has themodification. In some embodiments, the method further comprisesadministration of a third-generation AR inhibitor provided herein forinhibition of the mutant AR. In some embodiments, the subject hascancer. In some embodiments, the subject has a prostate cancer. In someembodiments, the subject has a castration resistant prostate cancer. Insome embodiments the CYP17A inhibitor is galeterone (TOK001), TAK-700 orabiraterone acetate. In some embodiments, the method further comprises astep of obtaining the nucleic acid sample from the subject.

In some embodiments, provided are methods for monitoring whether asubject receiving a second-generation AR antagonist for treatment of acancer has developed or will develop resistance to the therapy,comprising (a) assaying a sample containing a nucleic acid moleculeencoding an AR polypeptide from the subject to determine whether theencoded AR polypeptide is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; and (b) characterizing the subject as resistantor will become resistant to therapy with a second-generation ARantagonist if the subject has the modification. In some embodiments, themethod further comprises administration of a third-generation ARantagonist provided herein for inhibition of the mutant AR. In someembodiments, the subject has cancer. In some embodiments, the subjecthas a prostate cancer. In some embodiments, the subject has a castrationresistant prostate cancer. In some embodiments, the method furthercomprises a step of obtaining the nucleic acid sample from the subject.

In some embodiments, provided are methods for monitoring whether asubject receiving a first-generation AR antagonist for treatment of acancer has developed or will develop resistance to the therapy,comprising (a) assaying a sample containing a nucleic acid moleculeencoding an AR polypeptide from the subject to determine whether theencoded AR polypeptide is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; and (b) characterizing the subject as resistantor will become resistant to therapy with a first-generation ARantagonist if the subject has the modification. In some embodiments, themethod further comprises administration of a third-generation ARantagonist provided herein for inhibition of the mutant AR. In someembodiments, the subject has cancer. In some embodiments, the subjecthas a prostate cancer. In some embodiments, the subject has a castrationresistant prostate cancer. In some embodiments, the method furthercomprises a step of obtaining the nucleic acid sample from the subject.

In some embodiments, provided are methods for monitoring whether asubject receiving an AR antagonist that is a CYP17A inhibitor fortreatment of a cancer has developed or will develop resistance to thetherapy, comprising (a) assaying a sample containing a nucleic acidmolecule encoding an AR polypeptide from the subject to determinewhether the encoded AR polypeptide is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; and (b) characterizing the subject as resistantor will become resistant to therapy with an AR antagonist that is aCYP17A inhibitor if the subject has the modification. In someembodiments, the method further comprises administration of athird-generation AR antagonist provided herein for inhibition of themutant AR. In some embodiments, the subject has cancer. In someembodiments, the subject has a prostate cancer. In some embodiments, thesubject has a castration resistant prostate cancer. In some embodimentsthe CYP17A inhibitor is galeterone (TOK001), TAK-700 or abirateroneacetate. In some embodiments, the method further comprises a step ofobtaining the nucleic acid sample from the subject.

In some embodiments, provided are methods for optimizing the therapy ofa subject receiving a second-generation AR antagonist for treatment of acancer, comprising: (a) assaying a sample containing a nucleic acidmolecule encoding an AR polypeptide from the subject to determinewhether the encoded AR polypeptide is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; and (b) discontinuing treatment with thesecond-generation AR antagonist if the subject has the modification orcontinuing treatment with the second-generation AR antagonist if thesubject does not have the modification. In some embodiments, the methodfurther comprises a step of obtaining the nucleic acid sample from thesubject.

In some embodiments, provided are methods for optimizing the therapy ofa subject receiving a first-generation AR antagonist for treatment of acancer, comprising: (a) assaying a sample containing a nucleic acidmolecule encoding an AR polypeptide from the subject to determinewhether the encoded AR polypeptide is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; and (b) discontinuing treatment with thefirst-generation AR antagonist if the subject has the modification orcontinuing treatment with the first-generation AR antagonist if thesubject does not have the modification. In some embodiments, the methodfurther comprises a step of obtaining the nucleic acid sample from thesubject.

In some embodiments, provided are methods for optimizing the therapy ofa subject receiving an AR antagonist that is a CYP17A inhibitor fortreatment of a cancer, comprising: (a) assaying a sample containing anucleic acid molecule encoding an AR polypeptide from the subject todetermine whether the encoded AR polypeptide is modified at an aminoacid position corresponding to amino acid position 876 of the amino acidsequence set forth in SEQ ID NO: 1; and (b) discontinuing treatment withthe AR antagonist that is a CYP17A inhibitor if the subject has themodification or continuing treatment with the AR antagonist that is aCYP17A inhibitor if the subject does not have the modification. In someembodiments the CYP17A inhibitor is galeterone (TOK001), TAK-700 orabiraterone acetate. In some embodiments, the method further comprises astep of obtaining the nucleic acid sample from the subject.

In some embodiments, the modified AR is resistant to full antagonism bya second-generation AR antagonist, such as, for example, ARN-509,enzalutamide (MDV3100) or RD162. In some embodiments, asecond-generation AR antagonist, such as, for example, ARN-509,enzalutamide (MDV3100) or RD162 exhibits agonist activity toward themodified AR. In some embodiments, the modified AR is resistant to fullantagonism by a first-generation AR antagonist. In some embodiments, themodified AR is resistant to full antagonism by an AR antagonist that isa CYP17A.

In some embodiments, the subject has an AR dependent or AR mediateddisease or condition. In some embodiments, the AR dependent or ARmediated disease or condition is benign prostate hyperplasia, hirsutism,acne, adenomas and neoplasms of the prostate, benign or malignant tumorcells containing the AR, hyperpilosity, seborrhea, endometriosis,polycystic ovary syndrome, androgenic alopecia, hypogonadism,osteoporosis, suppression of spermatogenesis, libido, cachexia,anorexia, androgen supplementation for age related decreasedtestosterone levels, prostate cancer, breast cancer, bladder cancer,liver cancer, endometrial cancer, uterine cancer, hot flashes, Kennedy'sdisease, muscle atrophy and weakness, skin atrophy, bone loss, anemia,arteriosclerosis, cardiovascular disease, loss of energy, loss ofwell-being, type 2 diabetes or abdominal fat accumulation.

In some embodiments, the subject has cancer. In some embodiments, thesubject has a solid tumor. In some embodiments, the cancer is a prostatecancer, a breast cancer, a liver cancer, or a bladder cancer. In someembodiments, the cancer is a prostate cancer.

In some embodiments, the sample is from any tissue or fluid from anorganism. Samples include, but are not limited, to whole blood,dissociated bone marrow, bone marrow aspirate, pleural fluid, peritonealfluid, central spinal fluid, abdominal fluid, pancreatic fluid,cerebrospinal fluid, brain fluid, ascites, pericardial fluid, urine,saliva, bronchial lavage, sweat, tears, ear flow, sputum, hydrocelefluid, semen, vaginal flow, milk, amniotic fluid, and secretions ofrespiratory, intestinal or genitourinary tract. In particularembodiments, the sample is a tumor biopsy sample. In particularembodiments, the sample is from a fluid or tissue that is part of, orassociated with, the lymphatic system or circulatory system. In someembodiments, the sample is a blood sample that is a venous, arterial,peripheral, tissue, cord blood sample. In particular embodiments, thesample is a serum sample. In some embodiments, the sample contains oneor more circulating tumor cells (CTCs). In some embodiments, the samplecontains one or more disseminated tumor cells (DTC, e.g. in a bonemarrow aspirate sample).

Methods for the isolation of nucleic acids and proteins from cellscontained in tissue and fluid samples are well-known in the art. Inparticular embodiments, the nucleic acid sample obtained from thesubject is isolated from cells contained in a tumor biopsy from thesubject. In particular embodiments, the nucleic acid sample obtainedfrom the subject is isolated from cells in a bone marrow aspirate. Inparticular embodiments, the nucleic acid sample obtained from thesubject is isolated from cells contained serum sample. In particularembodiments, the nucleic acid sample obtained from the subject isisolated from cells contained lymph sample.

In some embodiments, the samples are obtained from the subject by anysuitable means of obtaining the sample using well-known and routineclinical methods. Procedures for obtaining fluid samples from a subjectare well known. For example, procedures for drawing and processing wholeblood and lymph are well-known and can be employed to obtain a samplefor use in the methods provided. Typically, for collection of a bloodsample, an anti-coagulation agent (e.g. EDTA, or citrate and heparin orCPD (citrate, phosphate, dextrose) or comparable substances) is added tothe sample to prevent coagulation of the blood. In some examples, theblood sample is collected in a collection tube that contains an amountof EDTA to prevent coagulation of the blood sample.

In some embodiments, the sample is a tissue biopsy and is obtained, forexample, by needle biopsy, CT-guided needle biopsy, aspiration biopsy,endoscopic biopsy, bronchoscopic biopsy, bronchial lavage, incisionalbiopsy, excisional biopsy, punch biopsy, shave biopsy, skin biopsy, bonemarrow biopsy, and the Loop Electrosurgical Excision Procedure (LEEP).Typically, a non-necrotic, sterile biopsy or specimen is obtained thatis greater than 100 mg, but which can be smaller, such as less than 100mg, 50 mg or less, 10 mg or less or 5 mg or less; or larger, such asmore than 100 mg. 200 mg or more, or 500 mg or more, 1 gm or more, 2 gmor more, 3 gm or more, 4 gm or more or 5 gm or more. The sample size tobe extracted for the assay depends on a number of factors including, butnot limited to, the number of assays to be performed, the health of thetissue sample, the type of cancer, and the condition of the patient. Insome embodiments, the tissue is placed in a sterile vessel, such as asterile tube or culture plate, and is optionally immersed in anappropriate media. Typically, the cells are dissociated into cellsuspensions by mechanical means and/or enzymatic treatment as is wellknown in the art. Typically, the cells are collected and then subjectedto standard procedures for the isolation of nucleic acid for the assay.

In some embodiments, the samples are obtained from the subject atregular intervals, such as, for example, one day, two days, three days,four days, five days, six days, one week, two weeks, weeks, four weeks,one month, two months, three months, four months, five months, sixmonths, one year, daily, weekly, bimonthly, quarterly, biyearly oryearly. In some embodiments, the collection of samples is performed at apredetermined time or at regular intervals relative to treatment withone or more anti-cancer agents. In some embodiments, the collection ofsamples is performed at a predetermined time or at regular intervalsrelative to treatment with an AR antagonist, such as a first- orsecond-generation AR antagonist. For example, a sample is collected at apredetermined time or at regular intervals prior to, during, orfollowing treatment or between successive treatments. In particularexamples, a sample is obtained from the subject prior to administrationof an anti-cancer therapy and then again at regular intervals aftertreatment has been effected. In particular examples, a sample isobtained from the subject prior to administration of an AR antagonist,such as a first- or second-generation AR antagonist, therapy and thenagain at regular intervals after treatment has been effected. In someembodiments, the AR antagonist is selected from among bicalutamide,flutamide, hydroxyflutamide, nilutamide, ARN-509, enzalutamide(MDV3100), and RD162. In some embodiments, the AR antagonist is a CYP17Ainhibitor. In some embodiments, the CYP17A inhibitor is selected fromamong galeterone (TOK001), TAK-700 or abiraterone acetate.

The volume of a fluid sample can be any volume that is suitable for thedetection of an AR mutant in the methods provided. In some examples, thevolume for the fluid sample is dependent on the particular assay methodused. For example, particular assay methods can require a larger orsmaller fluid sample volumes depending on factors such as, but notlimited to, the capacity of the device or method used and level ofthroughput of the assay method. In some examples a fluid sample isdiluted in an appropriate medium prior to application of the assaymethod. In some examples, a fluid sample is obtained from a subject anda portion or aliquot of the sample is used in the assay method. Theportion or aliquot can be diluted in an appropriate medium prior toapplication of the assay method.

In some embodiments, the sample is obtained from a subject that ismammal. Exemplary mammalian subjects include, but are not limited toprimates, such as humans, apes and monkeys; rodents, such as mice, rats,rabbits, and ferrets; ruminants, such as goats, cows, deer, and sheep;horses, pigs, dogs, cats, and other animals. In some embodiments, thesample is obtained from a patient. In some examples, the patient is ahuman patient.

In some embodiments, the nucleic acid sample obtained from the subjectis a genomic nucleic acid sample. In some embodiments, the nucleic acidsample obtained from the subject is an RNA sample. In some embodiments,mRNA is isolated from the total RNA in an RNA sample. In someembodiments, the RNA sample is reverse transcribed into cDNA. In someembodiments, the genomic nucleic acid sample is amplified by a nucleicacid amplification method. In some embodiments, the nucleic acidamplification method is polymerase chain reaction (PCR). In someembodiments, the genomic nucleic acid sample is amplified using a set ofnucleotide primers specific for the AR gene. In some embodiments, theset of nucleotide primers flank the nucleic acid sequence encoding aminoacid position 876 of the AR polypeptide. In some embodiments, theamplification product is a nucleic acid encoding amino acid position 876of the AR polypeptide. In some embodiments, a sequence specific primeris conjugated to a detectable molecule, such as a fluorescent label, abioluminescent label, a chemiluminescent label, a radiolabel, an enzymelabel, a detectable substrate, or a peptide or molecule that binds to asecond detectable molecule.

In some embodiments, assaying comprises sequencing the nucleic acidsample. In some embodiments, the nucleic acid encoding AR in a nucleicacid sample is first amplified by a method such as polymerase chainreaction (PCR) using sequence specific primers, and the amplified PCRfragment is then sequenced. Exemplary sequencing methods for use in themethods provide herein are well known in the art and include, but arenot limited to, dideoxy or chain termination methods, Maxam-Gilbertsequencing, massively parallel signature sequencing (or MPSS), polonysequencing, pyrosequencing, Illumina dye sequencing, SOLiD (orsequencing by ligation) sequencing, ion semiconductor sequencing, DNAnanoball sequencing, heliscope sequencing, and single molecule real time(SMRT) sequencing.

In some embodiments, the samples is a plasma or serum sample containingcirculating tumor DNA (ctDNA), RNA (ctRNA) or microRNA (see e.g. Chan etal. (2007) Br J Cancer. 96(5):681-5). In some embodiments, the DNAencoding the mutant AR is assessed by BEAMing (beads, amplification,emulsion, magnetic) PCR sequencing method (see, e.g. Li et al. (2006)Nat Methods. 3(2):95-7; Li et al. (2006) Nat Methods. 3(7):551-9; andDiehl et al. (2008) Nat Med. 14(9): 985-990). BEAMing is a technique inwhich individual DNA molecules are attached to magnetic beads inwater-in-oil emulsions and then subjected to compartmentalized PCRamplification. The mutational status of DNA bound to beads is thendetermined by hybridization to fluorescent allele-specific probes formutant or wild-type AR. Flow cytometry is then used to quantify, thelevel of mutant DNA present in the plasma or serum (see e.g. Higgins etal. (2012) Clin Cancer Res 18: 3462-3469).

In some embodiments, assaying a sample for detecting the presence of DNAencoding the mutant AR comprises detection of the mutation with asequence specific oligonucleotide probe that is specific for nucleicacid that encodes the mutant AR but not the wild-type AR. In someembodiments, assaying comprises (a) contacting a sample with a mutant ARnucleic acid sequence specific oligonucleotide probe, whereby if themutant nucleic acid sequence is present in the sample, a probe-DNAcomplex is formed, and (b) detecting the probe-DNA complex. In someembodiments, the oligonucleotide probe is specific for nucleic acidencoding leucine at a position corresponding to amino acid 876 of an ARpolypeptide. In some embodiments, the sequence specific probe isconjugated to a detectable molecule, such as a fluorescent label, abioluminescent label, a chemiluminescent label, a radiolabel, an enzymelabel, a detectable substrate, or a peptide or molecule that binds to asecond detectable molecule.

In some embodiments, single nucleotide changes are detectable by PCRusing PCR-based cleaved amplified polymorphic sequences (CAPS) markerswhich create restriction sites in the mutant sequences (Michaels et al(1998) Plant J. 14(3):381-5) or sequence specific hairpin probesattached to detectable moieties, such as, but not limited to, afluorophore (Mhlanga and Malmberg (2001) Methods 25:463-471). In someembodiments, the sequence specific probe is conjugated to a detectablemolecule, such as a fluorescent label, a bioluminescent label, achemiluminescent label, a radiolabel, an enzyme label, a detectablesubstrate, or a peptide or molecule that binds to a second detectablemolecule. In some embodiments, the oligonucleotide probe is specific fornucleic acid encoding leucine at a position corresponding to amino acid876 of an AR polypeptide.

In some embodiments, assaying a sample for detecting the presence of DNAencoding the mutant AR is performed using an oligonucleotide array (seee.g. Hastia et al. (1999) J Med Genet. 36(10):730-6). In someembodiments, the sample containing nucleic acid from the subject ishybridized directly to the chip. In some embodiments, the samplecontaining nucleic acid from the subject is amplified using anamplification method, such as, but not limited to polymerase chainreaction (PCR), and the amplified nucleic acid is hybridized to thechip. In some embodiments, the oligonucleotide array is contained on amicrochip. In some embodiments, single nucleotide changes are detectableusing microchips.

In some embodiments, assaying a sample comprises detection of themutation with an antibody specific for the mutant AR polypeptide. Insome embodiments, the method of detecting a mutant AR polypeptidecomprises obtaining a sample from a subject, wherein the samplecomprises an AR polypeptide and testing the sample for the presence of amutant AR polypeptide by contacting the sample with an antibody that isspecific for binding to the mutant AR polypeptide, and does not bind orbind with decreased affinity for the wild-type AR polypeptide, whereinthe presence of the mutant AR polypeptide creates an antibody-mutant ARpolypeptide complex. In some embodiments, the method further comprisesdetecting the antibody-mutant AR polypeptide complex. In someembodiments, the method further comprises detecting the antibody-mutantAR polypeptide complex with a detection reagent. In some embodiments,the mutant AR specific antibody is conjugated to a detectable molecule,such as a fluorescent label, a bioluminescent label, a chemiluminescentlabel, a radiolabel, an enzyme label, a detectable substrate, or apeptide or molecule that binds to a second detectable protein (e.g. asecondary antibody). In some embodiments, binding of the mutant ARspecific antibody is detected by assaying for the detectable molecule.In some embodiments, binding of the mutant AR specific antibody isdetected by using a secondary (e.g. anti-IgG) antibody. In someembodiments, the sample is a tumor biopsy sample, a bone marrowaspirate, a blood sample, a serum sample, or a lymph sample.

Identification of Molecules that Interact with Mutant Androgen Receptor

Provided herein are methods of using the mutant AR polypeptides forscreening of compounds that inhibit the mutant receptor (i.e.third-generation AR inhibitor compounds). In some embodiments, themethods are employed for the identification of third-generation ARinhibitor compounds for the treatment of cancer. In some embodiments,the methods are employed for the identification of third-generation ARinhibitor compounds for the treatment of resistant cancers, such asprostate cancer resistant to treatment with second-generation ARantagonists, such as ARN-509, enzalutamide (MDV3100) or RD162.

In some embodiments, a method for identifying third-generation ARinhibitor compounds comprises (a) expressing a mutant AR polypeptideprovided herein in a cell, (b) contacting the cell with a test compound,and (c) detecting the level of AR activity in the cell. In someembodiments, the cell is contacted with an AR agonist prior to or at thesame time as contacting the cell with the test compound. In someembodiments the cell is contacted with an AR agonist about 1 hour, 2,hours, 3 hours, 4 hours, 5 hours, 6 hours, 8 hours, 10 hours, 12 hours,14 hours, 16 hours, 18 hours, 20 hours, 22 hours, 24 hours or longerprior to contacting the cell with the test compound. In some embodimentsthe cell is contacted with an AR agonist at the same time as the cell iscontacted with test compound. In some embodiments, the AR agonist isselected from among methyltrienolone (R1881), DHT, mibolerone (Mb) andtestosterone. In some embodiments, the mutant AR polypeptide comprisesan amino acid substitution at a position corresponding to amino acidposition 876 of the wild-type AR polypeptide set forth in SEQ ID NO: 1.In some embodiments, the mutant AR polypeptide does not contain aphenylalanine at amino acid position 876 in the polypeptide. In someembodiments, the mutant AR polypeptide contains a leucine at amino acidposition 876 in the polypeptide.

In some embodiments, a cell line that can be transfected with nucleicacid encoding the mutant AR polypeptide and in which AR activity can bemonitored is used. In some embodiments, the cell does not express thewild-type AR. In some embodiments, the cell expresses a low level ofwild-type AR. In some embodiments, the cell expresses an endogenousmutant AR polypeptide. In some embodiments, the endogenous mutant ARpolypeptide comprises a modification at an amino acid corresponding toamino acid 877 of a wild-type AR polypeptide. In some embodiments, theendogenous mutant AR polypeptide comprises a modification that is asubstitution of Threonine to Alanine at amino acid position 877 (T877A).In some embodiments, the mutant AR polypeptide comprises a modificationat an amino acid corresponding to amino acid 874 of a wild-type ARpolypeptide. In some embodiments, the mutant AR polypeptide comprises amodification that is a substitution of Histidine to Tyrosine at aminoacid position 874 (H874Y). In some embodiments, the cell is a selectedfrom among HeLa, CV1, COS7, HepG2, HEK-293, DU145, PC3, and TSY-PR1. Insome embodiments, the cell line is a prostate cancer cell line. In someembodiments, the cell line is selected from among CWR, LNCaP, VCaP andLAPC4.

In some embodiments, the cell stably expresses the mutant ARpolypeptide. In some embodiments, the nucleic acid encoding the mutantAR is integrated into the genome of the cell. In some embodiments, thelevel of AR activity is detected using a reporter gene operably linkedto an AR-responsive promoter. In some embodiments, the AR-responsivepromoter comprises one or more androgen response elements (AREs) towhich the mutant AR polypeptide binds. In some embodiments, the promoteris selected from among a probasin (Pb), a prostate specific antigen(PSA), mouse mammary tumor virus long terminal repeat (MMTV LTR), fattyacid synthase (FASN), six transmembrane epithelial antigen of theprostate 4 (STEAP4), transmembrane protease, serine 2 (TMPRSS2),alpha-1-acid glycoprotein 1 (ORM1), or human homeobox gene NKX3.1promoter. In some embodiments, the promoter is a synthetic promotercontaining one or more AREs.

In some embodiments, the AR-responsive promoter is operably linked to asuitable reporter gene that encodes a detectable protein. Exemplarydetectable proteins include, but are not limited to, luciferase,fluorescent proteins, bioluminescent proteins, β-galactosidase, alkalinephosphatase, and chloramphenicol acetyltransferase. In some embodiments,a decrease in the expression of the reporter gene following exposure tothe test compound compared to a suitable control indicates that the testcompound is effective for inhibition of the mutant AR polypeptide. Insome embodiments, the control is basal expression of the reporter geneprior to exposure of the cell to the test compound. In some embodimentsthe expression of the reporter gene is assayed using a cell extractprepared from the test cells.

In some embodiments, the level of AR activity is detected by measuringthe expression of one or more endogenous androgen responsive genes in acell. In some embodiments, the androgen responsive gene is upregulated(i.e. induced) in response to androgen treatment. In some embodiments,the androgen responsive gene is downregulated (i.e. repressed) inresponse to androgen treatment. Exemplary androgen responsive genesinclude, but are not limited to, prostate specific antigen (PSA),prostate specific membrane antigen (PSMA), prostasin, snail homolog 2(SLUG), transmembrane protease, serine 2 (TMPRSS2), six transmembraneepithelial antigen of prostate family member 4 (STEAP4), FK506 bindingprotein 5 (FKBP5), orosomucoid 1/alpha-1-acid glycoprotein 1 (ORM1),solute carrier family 35 (SLC35F2/NOV), insulin-like growth factor I(IGF-1) IGF binding protein-3 and -5, CCAAT-enhancer binding protein-δ,phosphatase and tensin homolog deleted on chromosome 10 (PTEN), FASN,NKX3.1, AMIGO2, BDNF, CAMK2N1, HPGD, NCAPD3, PLD1, IL-15, IL-18, andERBB2/HER2.

In some embodiments, the level of AR activity is detected by measuringthe expression of one or more endogenous genes that are induced byexposure to an androgen or an AR agonist. In some embodiments, adecrease in the expression of one or more androgen inducible genesfollowing exposure to the test compound compared to a suitable controlindicates that the test compound is effective for inhibition of themutant AR polypeptide. Exemplary androgen inducible genes include butare not limited to, prostate specific antigen (PSA), prostasin, snailhomolog 2 (SLUG), transmembrane protease, serine 2 (TMPRSS2), sixtransmembrane epithelial antigen of prostate family member 4 (STEAP4).FK506 binding protein 5 (FKBP5), and orosomucoid 1/alpha-1-acidglycoprotein 1 (ORM1). In some embodiments, expression of the induciblegene is assessed in the presence of an AR agonist. In some embodiments,the cells are contacted with an androgen agonist prior to orsimultaneously with the test compound.

In some embodiments, the level of AR activity is detected by measuringthe expression of one or more endogenous genes that are repressed byexposure to an androgen or an AR agonist. In some embodiments, anincrease in or failure to repress the expression of one or more androgenrepressed genes following exposure to the test compound compared to asuitable control indicates that the test compound is effective forinhibition of the mutant AR polypeptide. In some embodiments, thecontrol is basal expression of the gene prior to exposure of the cell tothe test compound. Exemplary androgen repressed genes include, but arenot limited to, prostate specific membrane antigen (PSMA), solutecarrier family 35 (SLC35F2/NOV), IGF binding protein-3 and -5,CCAAT-enhancer binding protein-6, phosphatase and tensin homolog deletedon chromosome 10 (PTEN). IL-15, IL-18, and ERBB2/HER2. In someembodiments, expression of the repressible gene is assessed in thepresence of an AR agonist. In some embodiments, the cells are contactedwith an androgen agonist prior to or simultaneously with the testcompound.

Methods to measure the expression of endogenous genes is well-known inthe art. Exemplary methods for the measurement of gene expressioninclude, but are not limited to protein analytical methods such as, forexample, immunohistochemistry, immunoblotting (e.g. Western analysis),chromatography, and nucleic acids analytical methods, such as, forexample, polymerase chain reaction (PCR), quantitative PCR (qPCR), realtime PCR (RT-PCR), Northern analysis.

In some embodiments, the activity of a mutant AR polypeptide is measuredusing an assay such as, but not limited to, a AR coactivator bindingassay (e.g. immunoprecipitation assays, two-hybrid assays, Förster(fluorescence) resonance energy transfer assays, for example,LanthaScreen™ TR-FRET androgen receptor coactivator assay), a ARconformational profiling assay (see, e.g., Joseph et al. (2009) PNAS106(29): 12178-12183), an AR DNA binding assay (see, e.g., Roche et al.(1992) Mol. Endocrinol. 6(12):2229-35), chromatin immunoprecipitation,N/C terminal interaction assay (see, e.g., Hsu et al. (2005) Mol.Endocrinology 19(2) 350-361 and Ghali et al. (2003) J Clin EndocrinolMetab. 88(5):2185-93).

In some embodiments, a method for identifying third-generation ARinhibitor compounds comprises selecting a potential third-generation ARinhibitor compound using computer-assisted modeling with athree-dimensional crystal or solution structure of a mutant ARpolypeptide provided herein. In some embodiments, the mutant ARpolypeptide comprises an amino acid substitution at a positioncorresponding to amino acid position 876 of the wild-type AR polypeptideset forth in SEQ ID NO: 1. In some embodiments, the mutant ARpolypeptide does not contain a phenylalanine at amino acid position 876in the polypeptide. In some embodiments, the mutant AR polypeptidecontains a leucine at amino acid position 876 in the polypeptide. Insome embodiments, the method comprises contacting the mutant ARpolypeptide with the test compound and detecting the interaction of thetest compound with the mutant AR polypeptide. In some embodiments, atest compound that interacts with the mutant AR polypeptide isidentified as a candidate third-generation AR inhibitor compound.

In some embodiments, a test compound for use in the methods provided isa member of a library of compounds. In some embodiments, generation of alibrary of test compounds is by any suitable method for the productionof chemical compounds. A “library of test compounds” refers to a panelcomprising a multiplicity of test compounds. An exemplary approach forthe synthesis of molecular libraries of small organic molecules has beendescribed (Carell et al. (1994). Angew. Chem. Int. Ed. Engl. 33:2059;Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061). In someembodiments the test compounds provided herein are obtained using any ofthe numerous approaches in combinatorial library methods known in theart, including: biological libraries; spatially addressable parallelsolid phase or solution phase libraries, synthetic library methodsrequiring deconvolution, the ‘one-bead one-compound’ library method, andsynthetic library methods using affinity chromatography selection. Thebiological library approach is limited to peptide libraries, while theother four approaches are applicable to peptide, non-peptide oligomer orsmall molecule libraries of compounds (Lam, K. S. (1997) Anticancer DrugDes. 12:145). Other exemplary methods for the synthesis of molecularlibraries are found in the art, for example in: Erb et al. (1994). Proc.Natl. Acad. Sci. USA 91:11422; Horwell et al. (1996) Immunopharmacology33:68-; and in Gallop et al. (1994): J. Med. Chem. 37:1233-. In someembodiments, libraries of compounds are presented in solution (e.g.,Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991)Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria(Ladner U.S. Pat. No. 5,223,409), spores (Ladner USP '409), plasmids(Cull et al. (1992) Proc Natl Acad Sci USA 89:1865-1869) or on phage(Scott and Smith (1990) Science 249:386-390); (Devlin (1990) Science249:404-406); (Cwirla et al. (1990) Proc. Natl. Acad. Sci.87:6378-6382); (Felici (1991) J. Mol. Biol. 222:301-310). In someembodiments, combinatorial polypeptides are produced from a cDNAlibrary. Exemplary compounds that can be screened for activity include,but are not limited to, peptides, nucleic acids, carbohydrates, smallorganic molecules, and natural product extract libraries.

AR Inhibitors Identified by the Screening Methods

The third-generation AR inhibitors identified using the screeningmethods provided herein are AR modulators. In some embodiments, thethird-generation AR inhibitor inhibits or reduces at least one activityof an AR polypeptide. Exemplary AR activities include, but are notlimited to, co-activator binding, DNA binding, ligand binding, ornuclear translocation. In some embodiments, the third-generation ARinhibitor inhibits an activity of an AR polypeptide by about 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98% or 100% compared to theactivity of the AR polypeptide in the absence of the inhibitor. In someembodiments, the third-generation AR inhibitor compounds identifiedusing the methods provided herein are AR inverse agonists. ARantagonists. AR degraders, AR trafficking modulators and/or ARDNA-binding inhibitors. In some embodiments, a third-generation ARinhibitor compounds identified using the methods provided herein is anAR inverse agonist. In some embodiments, the third-generation ARinhibitor compounds identified using the methods provided herein are ARantagonists. In some embodiments, the third-generation AR inhibitorcompounds identified using the methods provided herein are AR degraders.In some embodiments, the third-generation AR inhibitor compoundsidentified using the methods provided herein are AR traffickingmodulators. In some embodiments, the third-generation AR inhibitorcompounds identified using the methods provided herein are ARDNA-binding inhibitors. In some embodiments, the AR inhibitor inhibitsat least one activity of a wild-type AR polypeptide. In someembodiments, the AR inhibitor inhibits at least one activity of a mutantAR polypeptide. In some embodiments, the third-generation AR inhibitorcompound identified using the methods provided herein has minimalpro-convulsant activity and/or minimal impact on seizure threshold. Insome embodiments, the third-generation AR inhibitor compound identifiedusing the methods provided herein displays minimal modulation of theGABA-gated chloride channel. In some embodiments, the third-generationAR inhibitor compound identified using the methods provided hereindisplays minimal binding to the GABA-gated chloride channel. In someembodiments, the third-generation AR inhibitor compound identified usingthe methods provided herein has minimal antagonism of the GABA-gatedchloride channel. In some embodiments, the third-generation AR inhibitorcompound identified using the methods provided herein is an AR modulatorwith minimal interaction with a GABA-gated chloride channel. In someembodiments, the third-generation AR inhibitor compound identified usingthe methods provided herein is an AR modulator with minimal interactionwith the GABA_(A)-gated chloride channel. In some embodiments, thethird-generation AR inhibitor compound identified using the methodsprovided herein is an AR modulator with minimal interaction with theGABA_(A)-gated chloride channel and or minimal blood-brain barrierpenetration. GABA assays are known and include, but are not limited to,those described in Ashok K. Mehta and Maharaj K. Ticku “Characterizationof the Picrotoxin Site of GABA_(A) Receptors” Current Protocols inPharmacology (2000) 1.18.1-1.18.17; Copyright © 2000 by John Wiley &Sons, Inc., which is herein incorporated by reference.

In some embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein inhibits AR nuclear translocation. Insome embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein inhibits AR DNA binding to androgenresponse elements. In some embodiments, a third-generation AR inhibitorcompound identified using the methods provided herein inhibitscoactivator recruitment at an AR responsive promoter. In someembodiments, a third-generation AR inhibitor compound identified usingthe methods provided herein exhibits no agonist activity inAR-overexpressing prostate cancer cells.

In some embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein inhibits growth of castrationsensitive and castration resistant prostate cancer xenograft models. Insome embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein inhibits growth of castrationsensitive and castration resistant prostate cancer xenograft modelsexpressing wild-type AR. In some embodiments, a third-generation ARinhibitor compound identified using the methods provided herein inhibitsgrowth of castration sensitive and castration resistant prostate cancerxenograft models expressing a mutant AR having a F876L mutation. In someembodiments, a third-generation AR inhibitor compound identified usingthe methods provided herein inhibits growth of castration sensitive andcastration resistant prostate cancer xenograft models expressing thewild-type AR and a mutant AR having a F876L mutation. In someembodiments, a third-generation AR inhibitor compound identified usingthe methods provided herein inhibits growth of castration sensitive andcastration resistant prostate cancer xenograft models expressing amutant AR having a T877A mutation (e.g. xenograft tumors formed fromLNCaP cells). In some embodiments, a third-generation AR inhibitorcompound identified using the methods provided herein inhibits growth ofcastration sensitive and castration resistant prostate cancer xenograftmodels expressing the wild-type AR and a mutant AR having a T877Amutation (e.g. xenograft tumors formed from LNCaP/AR cells). In someembodiments, a third-generation AR inhibitor compound identified usingthe methods provided herein inhibits growth of castration sensitive andcastration resistant prostate cancer xenograft models expressing amutant AR having a T877A mutation and a mutant AR having a F876Lmutation.

Pharmaceutical Compositions

In some embodiments, provided is a pharmaceutical composition comprisinga therapeutically effective amount of a third-generation AR inhibitoridentified using the screening methods provided herein. In someembodiments, provided is a use of a third-generation AR inhibitoridentified using the screening methods provided herein for thepreparation of a medicament.

In some embodiments, the pharmaceutical composition comprising athird-generation AR inhibitor also contains at least onepharmaceutically acceptable inactive ingredient. In some embodiments,the pharmaceutical composition comprising a third-generation ARinhibitor is formulated for intravenous injection, subcutaneousinjection, oral administration, or topical administration. In someembodiments, the pharmaceutical composition comprising athird-generation AR inhibitor is a tablet, a pill, a capsule, a liquid,a suspension, a gel, a colloid, a dispersion, a suspension, a solution,an emulsion, an ointment, or a lotion.

Pharmaceutical compositions are formulated in a conventional mannerusing one or more pharmaceutically acceptable inactive ingredients thatfacilitate processing of the active compounds into preparations that canbe used pharmaceutically. Proper formulation is dependent upon the routeof administration chosen. A summary of pharmaceutical compositionsdescribed herein can be found, for example, in Remington: The Scienceand Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack PublishingCompany, 1995); Hoover, John E., Remington's Pharmaceutical Sciences.Mack Publishing Co., Easton, Pa. 1975; Liberman, H. A. and Lachman, L.,Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N.Y., 1980;and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed.(Lippincott Williams & Wilkins 1999), herein incorporated by referencefor such disclosure.

Provided herein are pharmaceutical compositions a third-generation ARinhibitor, or a pharmaceutically acceptable salt thereof, and at leastone pharmaceutically acceptable inactive ingredient. In someembodiments, the third-generation AR inhibitor described herein isadministered as pharmaceutical compositions in which thethird-generation AR inhibitor is mixed with other active ingredients, asin combination therapy. In other embodiments, the pharmaceuticalcompositions include other medicinal or pharmaceutical agents, carriers,adjuvants, preserving, stabilizing, wetting or emulsifying agents,solution promoters, salts for regulating the osmotic pressure, and/orbuffers. In yet other embodiments, the pharmaceutical compositionsinclude other therapeutically valuable substances.

A pharmaceutical composition, as used herein, refers to a mixture of athe third-generation AR inhibitor or a pharmaceutically acceptable saltthereof, with other chemical components (i.e. pharmaceuticallyacceptable inactive ingredients), such as carriers, excipients, binders,filling agents, suspending agents, flavoring agents, sweetening agents,disintegrating agents, dispersing agents, surfactants, lubricants,colorants, diluents, solubilizers, moistening agents, plasticizers,stabilizers, penetration enhancers, wetting agents, anti-foaming agents,antioxidants, preservatives, or one or more combination thereof. Thepharmaceutical composition facilitates administration of the compound toa subject, such as a mammal.

A therapeutically effective amount can vary widely depending on theseverity of the disease, the age and relative health of the subject, thepotency of the compound used and other factors. The compounds can beused singly or in combination with one or more therapeutic agents ascomponents of mixtures.

The pharmaceutical formulations described herein are administered to asubject by appropriate administration routes, including but not limitedto, oral, parenteral (e.g., intravenous, subcutaneous, intramuscular),intranasal, buccal, topical, rectal, or transdermal administrationroutes. The pharmaceutical formulations described herein include, butare not limited to, aqueous liquid dispersions, self-emulsifyingdispersions, solid solutions, liposomal dispersions, aerosols, soliddosage forms, powders, immediate release formulations, controlledrelease formulations, fast melt formulations, tablets, capsules, pills,delayed release formulations, extended release formulations, pulsatilerelease formulations, multiparticulate formulations, and mixed immediateand controlled release formulations.

In some embodiments, the pharmaceutical composition further comprisesone or more additional therapeutically active agents, including, but notlimited to, corticosteroids, anti-emetic agents, analgesics, anti-canceragents, anti-inflammatory agents, kinase inhibitors, HSP90 inhibitors,and histone deacetylase (HDAC) inhibitors.

In some embodiments, provided is a pharmaceutical composition comprisinga therapeutically effective amount of a mutant AR polypeptide providedherein. In some embodiments, provided is a pharmaceutical compositioncomprising a therapeutically effective amount of a nucleic acid encodinga mutant AR polypeptide provided herein.

Therapeutic Methods

In some embodiments, the third-generation AR inhibitor compoundsidentified using the methods provided herein are administered for thetreatment of a disease or condition. In some embodiments, describedherein are methods of treating an AR dependent or AR mediated disease orcondition in mammal comprising administering to the mammal atherapeutically effective amount of a third-generation AR inhibitorcompound identified using the methods provided herein, or apharmaceutically acceptable salt thereof.

In some embodiments, provided are methods comprising administering athird-generation AR inhibitor compound identified using the methodsprovided herein to a subject (e.g. a human) having a disease orcondition that is AR meditated or AR dependent. In some embodiments,provided is a use of a third-generation AR inhibitor compound identifiedusing the methods provided herein for the preparation of medicament forthe treatment of a disease or condition that is AR meditated or ARdependent. In some embodiments, provided is a third-generation ARinhibitor compound identified using the methods provided herein for thetreatment of a disease or condition that is AR meditated or ARdependent. In some embodiments, the subject (e.g. a human) is currentlyreceiving one or more additional therapeutically active agents otherthan the third-generation AR inhibitor compound.

In some embodiments, the method further comprises administering one ormore additional therapeutically active agents other than athird-generation AR inhibitor compound identified using the methodsprovided herein. In some embodiments, the one or more additionaltherapeutically active agents other than a third-generation AR inhibitorcompound identified using the methods provided herein are selected from:hormones, hormone receptor agonists or antagonists, corticosteroids,anti-emetic agents, analgesics, anti-cancer agents, anti-inflammatoryagents, kinase inhibitors, HSP90 inhibitors, histone deacetylase (HDAC)inhibitors. In some embodiments, third-generation AR inhibitor compoundis administered prior to, simultaneously, following, or intermittentlywith the one or more additional therapeutically active agents other thanthe third-generation AR inhibitor compound.

In some embodiments, the subject is administered agonadotropin-releasing hormone (GnRH) agonist or antagonist incombination with third-generation AR inhibitor compound provided herein.In some embodiments, a GnRH receptor agonist such as leuprolide,bruserelin and goserelin is administered to a subject in combinationwith third-generation AR inhibitor compound provided herein. GnRHreceptor agonists cause an initial surge in hormone production (i.e.“clinical flare”) followed by the inhibition of lutenizing hormoneproduction, which in turn causes a suppression of testosterone anddihydrotestosterone, on which continued growth of prostate cancer cellsdepend. In some embodiments, the subject is administered agonadotropin-releasing hormone (GnRH) agonist or antagonist incombination with third-generation AR inhibitor compound provided hereinfor the treatment of an AR dependent or AR mediated disease or conditionsuch as a prostate, breast, bladder or hepatocellular cancer. In someembodiments, the subject is administered a gonadotropin-releasinghormone (GnRH) agonist or antagonist in combination withthird-generation AR inhibitor compound provided herein for the treatmentof a castration resistant prostate cancer (CRPC). In some embodiments,the subject is administered a third-generation AR inhibitor compoundprovided herein to reduce or inhibit the initial surge in hormoneproduction caused by treatment with a GnRH receptor agonist. In someembodiments, third-generation AR inhibitor compound is administeredprior to, simultaneously, following, or intermittently with a GnRHreceptor agonist or antagonist.

In some embodiments, the AR dependent or AR mediated disease orcondition is benign prostate hyperplasia, hirsutism, acne, adenomas andneoplasms of the prostate, benign or malignant tumor cells containingthe androgen receptor, hyperpilosity, seborrhea, endometriosis,polycystic ovary syndrome, androgenic alopecia, hypogonadism,osteoporosis, suppression of spermatogenesis, libido, cachexia,anorexia, androgen supplementation for age related decreasedtestosterone levels, prostate cancer, breast cancer, endometrial cancer,uterine cancer, bladder cancer, hepatocellular cancer, hot flashes, andKennedy's disease, muscle atrophy and weakness, skin atrophy, bone loss,anemia, arteriosclerosis, cardiovascular disease, loss of energy, lossof well-being, type 2 diabetes or abdominal fat accumulation. In someembodiments, the AR dependent or AR mediated disease or condition is anAR dependent or AR mediated cancer, such as, for example, a prostate,breast, bladder or liver (i.e. hepatocellular) cancer.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof. In some embodiments, the cancer is a hormone dependent cancer.In some embodiments, the hormone dependent cancer is an AR dependentcancer. In some embodiments, the cancer is prostate cancer. In someembodiments, the cancer is castration resistant prostate cancer. In someembodiments, the method of treating cancer further comprisesadministering to the mammal at least one additional anti-cancer agent.

In some embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein is used to treat prostate cancer in amammal, wherein the mammal has not received treatment with ananti-cancer agent. In some embodiments, a third-generation AR inhibitorcompound identified using the methods provided herein is used to treatprostate cancer in a mammal, wherein the mammal has not receivedtreatment with a chemotherapeutic compound.

In some embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein is used to treat prostate cancer in amammal, wherein the mammal has been administered one or more anti-canceragents. Exemplary anti-cancer agents include, but are not limited to,hormonal therapeutic agents, including, but not limited to first- andsecond-generation AR antagonists (e.g. bicalutamide, flutamide,hydroxyflutamide, nilutamide, ARN-509, enzalutamide (MDV3100) and RD162)and compounds that inhibit hormone (e.g. androgen) production, such as,for example, galeterone (TOK001). TAK-700 or abiraterone acetate,chemotherapeutic compounds, anti-metabolites, anti-cancer antibodies,surgery, radiation, and hyperthermal therapy. In some embodiments, athird-generation AR inhibitor compound identified using the methodsprovided herein is used to treat prostate cancer in a mammal, whereinthe mammal has been administered one or more chemotherapeutic compounds.In some embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein is used to treat prostate cancer in amammal, wherein the mammal has been treated by surgery. In someembodiments, a third-generation AR inhibitor compound identified usingthe methods provided herein is used to treat prostate cancer in amammal, wherein the mammal has been treated with radiation therapy. Insome embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein is used to treat prostate cancer in amammal, wherein the mammal has been treated with a hyperthermal therapy.

In some embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein is used to treat prostate cancer in amammal, wherein the mammal has been administered one or more cycles oftreatment with an anti-cancer agent.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof, wherein the compound is an AR inverse agonist, AR antagonist,an AR degrader, an AR trafficking modulator, an AR DNA-bindinginhibitor, or combinations thereof.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof, wherein the compound is an AR inverse agonist.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof, wherein the compound is an AR antagonist.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof, wherein the compound is an AR degrader.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof, wherein the compound is an AR trafficking modulator.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof, wherein the compound is an AR DNA-binding inhibitor.

In some embodiments, described herein are methods of treating cancer ina mammal comprising administering to the mammal a therapeuticallyeffective amount of a third-generation AR inhibitor compound identifiedusing the methods provided herein, or a pharmaceutically acceptable saltthereof, wherein the compound is an AR protein synthesis inhibitor.

In some embodiments, the cancer is prostate cancer. In some embodiments,the cancer is castration resistant prostate cancer. In some embodiments,the prostate cancer is an ARN-509-resistant prostate cancer. In someembodiments, the prostate cancer is an enzalutamide (MDV3100)-resistantprostate cancer. In some embodiments, the prostate cancer is anRD162-resistant prostate cancer. In some embodiments, the prostatecancer is an abiraterone acetate-resistant prostate cancer. In someembodiments, the prostate cancer is a galeterone (TOK001)-resistantprostate cancer. In some embodiments, the prostate cancer is aTAK-700-resistant prostate cancer.

Pharmaceutical formulations described herein are administrable to asubject in a variety of ways by multiple administration routes,including but not limited to, oral, parenteral (e.g., intravenous,subcutaneous, intramuscular), buccal, topical or transdermaladministration routes. The pharmaceutical formulations described hereininclude, but are not limited to, aqueous liquid dispersions,self-emulsifying dispersions, solid solutions, liposomal dispersions,solid dosage forms, powders, immediate release formulations, controlledrelease formulations, fast melt formulations, tablets, capsules, pills,delayed release formulations, extended release formulations, pulsatilerelease formulations, multiparticulate formulations, and mixed immediateand controlled release formulations. In some embodiments, athird-generation AR inhibitor compound identified using the methodsprovided herein is administered orally. In some embodiments, athird-generation AR inhibitor compound identified using the methodsprovided herein is administered intravenously.

In some embodiments, a third-generation AR inhibitor compound identifiedusing the methods provided herein is administered topically. In suchembodiments, a third-generation AR inhibitor compound identified usingthe methods provided herein is formulated into a variety of topicallyadministrable compositions, such as solutions, suspensions, lotions,gels, pastes, shampoos, scrubs, rubs, smears, medicated sticks,medicated bandages, balms, creams or ointments. Such pharmaceuticalcompounds can contain solubilizers, stabilizers, tonicity enhancingagents, buffers and preservatives. In one aspect, the anti-androgencompound identified using the methods provided herein is administeredtopically to the skin.

In another aspect is the use of a third-generation AR inhibitor compoundidentified using the methods provided herein in the manufacture of amedicament for treating a disease, disorder or conditions in which theactivity of AR contributes to the pathology and/or symptoms of thedisease or condition. In one aspect, the disease or condition is any ofthe diseases or conditions specified herein.

In any of the aforementioned aspects are further embodiments in which:(a) the effective amount of the third-generation AR inhibitor compoundidentified using the methods provided herein is systemicallyadministered to the mammal; and/or (b) the effective amount of thethird-generation AR inhibitor compound is administered orally to themammal; and/or (c) the effective amount of the third-generation ARinhibitor compound is intravenously administered to the mammal; and/or(d) the effective amount of the third-generation AR inhibitor compoundis administered by injection to the mammal; and/or (e) the effectiveamount of the third-generation AR inhibitor compound is administeredtopically to the mammal; and/or (f) the effective amount of thethird-generation AR inhibitor compound is administered non-systemicallyor locally to the mammal.

In any of the aforementioned aspects are further embodiments comprisingsingle administrations of the effective amount of the third-generationAR inhibitor compound identified using the methods provided herein,including further embodiments in which (i) the third-generation ARinhibitor compound is administered once; (ii) the third-generation ARinhibitor compound is administered to the mammal multiple times over thespan of one day; (iii) continually; or (iv) continuously.

In any of the aforementioned aspects are further embodiments comprisingmultiple administrations of the effective amount of a third-generationAR inhibitor compound identified using the methods provided herein,including further embodiments in which (i) the third-generation ARinhibitor compound is administered continuously or intermittently: as ina single dose; (ii) the time between multiple administrations is every 6hours; (iii) the third-generation AR inhibitor compound is administeredto the mammal every 8 hours; (iv) the third-generation AR inhibitorcompound is administered to the mammal every 12 hours; (v) thethird-generation AR inhibitor compound is administered to the mammalevery 24 hours. In further or alternative embodiments, the methodcomprises a drug holiday, % herein the administration of thethird-generation AR inhibitor compound is temporarily suspended or thedose of the compound being administered is temporarily reduced; at theend of the drug holiday, dosing of the compound is resumed. In someembodiments, the length of the drug holiday varies from 2 days to 1year.

Also provided are methods of reducing AR activation in a mammalcomprising administering to the mammal a third-generation AR inhibitorcompound identified using the methods provided herein. In someembodiments, the method comprises reducing AR activation in prostatecells in the mammal. In some embodiments, the method comprises reducingAR activation in non-prostate cells. In some embodiments, the method ofreducing AR activation comprises reducing the binding of androgens tothe androgen receptor. In some embodiments, the method of reducing ARactivation comprises reducing AR concentration in a cell.

In some cases disclosed herein is the use of a third-generation ARinhibitor compound identified using the methods provided herein in themanufacture of a medicament for the treatment of diseases or conditionsthat are AR dependent or AR mediated. In some embodiments, the diseaseor condition is prostate cancer. In some embodiments, the AR dependentor AR mediated disease or condition is described herein.

In some cases disclosed herein is the use of a third-generation ARinhibitor compound identified using the methods provided herein in thetreatment or prevention of diseases or conditions that are AR dependentor AR mediated. In some embodiments, the AR dependent or AR mediateddisease or condition is described herein.

In any of the embodiments disclosed herein, the mammal is a human. Insome embodiments, the third-generation AR inhibitor compound providedherein is administered to a human.

In some embodiments, the third-generation AR inhibitor compound providedherein is used to diminish, reduce, or eliminate the activity of AR.

In some embodiments, the third-generation AR inhibitor compoundsidentified by the methods disclosed herein are selective AR modulators.In some embodiments, the third-generation AR inhibitor compoundsidentified by the methods disclosed herein have high specificity for theAR and have desirable, tissue-selective pharmacological activities.Desirable, tissue-selective pharmacological activities include, but arenot limited to, AR antagonist activity in prostate cells and no ARantagonist activity in non-prostate cells. In some embodiments, thethird-generation AR inhibitor compounds disclosed herein areanti-androgens that display negligible or no AR agonist activity.

In some embodiments, presented herein are third-generation AR inhibitorcompounds identified by the methods disclosed herein selected fromactive metabolites, tautomers, pharmaceutically acceptable solvates,pharmaceutically acceptable salts or prodrugs of an AR inhibitorcompound identified using the methods provided herein.

In some embodiments, the pharmaceutical composition comprisingthird-generation AR inhibitor compounds is administered in combinationwith one or more additional therapeutic agents, including, but notlimited to, corticosteroids, anti-emetic agents, analgesics, anti-canceragents, anti-inflammatory agents, kinase inhibitors. HSP90 inhibitors,and histone deacetylase (HDAC) inhibitors. In some embodiments, thepharmaceutical composition comprising third-generation AR inhibitorcompounds is administered in combination with an anti-cancer agentincluding, but not limited to, a hormonal therapeutic agent, including,but not limited to a first- and second-generation AR antagonists (e.g.bicalutamide, flutamide, hydroxyflutamide, nilutamide, ARN-509,enzalutamide (MDV3100) and RD162), a compound that inhibits hormone(e.g. androgen) production, such as a CYP17A inhibitor, including, forexample, galeterone (TOK001), TAK-700 or abiraterone acetate,chemotherapeutic compounds, anti-metabolites, anti-cancer antibodies,surgery, radiation, and hyperthermal therapy. In some embodiments, thethird-generation AR inhibitor compound and the additional therapeuticagent is administered in the same composition. In some embodiments, thethird-generation AR inhibitor compound and the additional therapeuticagent are administered as separate compositions. In some embodiments,the third-generation AR inhibitor compound and the additionaltherapeutic agent are administered simultaneously, sequentially, orintermittently. In some embodiments, the third-generation AR inhibitorcompound and the additional therapeutic agent are administered by thesame route of administration. In some embodiments, the third-generationAR inhibitor compound and the additional therapeutic agent areadministered by different routes of administration.

Kits/Articles of Manufacture

For use in the diagnostic and therapeutic applications described herein,kits and articles of manufacture are also described herein. Such kitscan comprise a carrier, package, or container that is compartmentalizedto receive one or more containers such as vials, tubes, and the like,each of the container(s) comprising one of the separate elements to beused in a method described herein. Suitable containers include, forexample, bottles, vials, syringes, and test tubes. The containers areformed from any acceptable material including, e.g., glass or plastic.

In some embodiments, the kits provided herein are for use in detectingnucleic acid encoding a mutant AR polypeptide in a subject or fordetecting a mutant AR polypeptide in a subject (i.e. a diagnostic kit).In some embodiments the kits are employed for selecting patients fortreatment with a third-generation AR antagonist, for identifyingsubjects as resistant or likely to become resistant to a first- orsecond-generation AR antagonist, for monitoring the development ofresistance to a first- or second-generation AR antagonist therapy, orcombinations thereof. The kits provided herein contain one or morereagents for the detection of the nucleic acid encoding a mutant ARpolypeptide, for the detection of mutant AR polypeptides, for detectionof AR activity in cells from the subject, or combinations thereof.Exemplary reagents include but are not limited to, buffers, PCRreagents, antibodies, substrates for enzymatic staining, chromagens orother materials, such as slides, containers, microtiter plates, andoptionally, instructions for performing the methods. Those of skill inthe art will recognize many other possible containers and plates andreagents that can be used for contacting the various materials. Kitsalso can contain control samples, such as for example, nucleic acids orproteins, such as for example a mutant AR polypeptide provided herein ornucleic acids encoding a mutant AR polypeptide provided herein. In someembodiments, kits contain one or more set of oligonucleotide primers fordetection of endogenous androgen gene expression.

In some embodiments, the container(s) can comprise one or more first- orsecond-generation AR antagonists or third-generation AR inhibitorcompounds identified by the methods described herein, optionally in acomposition or in combination with another agent as disclosed herein.The container(s) optionally have a sterile access port (for example thecontainer can be an intravenous solution bag or a vial having a stopperpierceable by a hypodermic injection needle). Such kits optionallycomprising a compound with an identifying description or label orinstructions relating to its use in the methods described herein.

A kit will typically comprise one or more additional containers, eachwith one or more of various materials (such as reagents, optionally inconcentrated form, and/or devices) desirable from a commercial and userstandpoint for use of a compound described herein. Non-limiting examplesof such materials include, but not limited to, buffers, diluents,filters, needles, syringes; carrier, package, container, vial and/ortube labels listing contents and/or instructions for use, and packageinserts with instructions for use. A set of instructions will alsotypically be included.

A label can be on or associated with the container. A label can be on acontainer when letters, numbers or other characters forming the labelare attached, molded or etched into the container itself; a label can beassociated with a container when it is present within a receptacle orcarrier that also holds the container, e.g., as a package insert. Alabel can be used to indicate that the contents are to be used for aspecific therapeutic application. The label can also indicate directionsfor use of the contents, such as in the methods described herein.

Articles of manufacture, which include packaging material, athird-generation AR inhibitor compound identified using the methodsprovided herein within the packaging material, and a label thatindicates that the compound or composition, or pharmaceuticallyacceptable salt, tautomers, pharmaceutically acceptable N-oxide,pharmaceutically active metabolite, pharmaceutically acceptable prodrug,or pharmaceutically acceptable solvate thereof, is used for reducing,diminishing or eliminating the effects of androgen receptors, or for thetreatment, prevention or amelioration of one or more symptoms of adisease or condition that would benefit from a reduction or eliminationof androgen receptor activity, are provided.

Production of Anti-Androgen Resistant Cell Lines

Provided herein are methods for producing prostate cancer cell linesresistant to treatment with an AR antagonist. In some embodiments, theprostate cancer cell lines are resistant to treatment with ARN-509. Insome embodiments, the prostate cancer cell lines are resistant totreatment with enzalutamide (MDV3100). In some embodiments, theresistant cell lines generated by the method provided express a higherlevel of AR compared to the parental cell line used to generate theresistant cell line. In some embodiments, the resistant cell linesgenerated by the method express about 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5,5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10 times or greater the amount ofAR compared to the parental cell line. In some embodiments, theresistant cell lines express a mutant AR protein.

In some embodiments, the method comprises contacting a prostate cancercell line (i.e. parental cell line) with an AR antagonist and culturingthe cells for a predetermined period of time. In some embodiments, themethod comprises culturing the cells in increasing concentrations of theAR antagonist for a predetermined period of time. In some embodiments,the concentration of the AR antagonist ranges from about 0.1 μM to about100 μM, such as, for example, 1 μM to about 10 μM. In some embodiments,the cells are cultured at 0.8 μM, 1.5 μM, 3 μM and 6 μM of the ARantagonist. In some embodiments, the concentration of the AR antagonistis increased 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times. In someembodiments, the concentration of the AR antagonist is increased 3times. In some embodiments, the cells are cultured in the presence ofthe AR antagonist 1 day, 2 days, 3, days, 4 days, 5 days, 6 days, 1week, 2 weeks, 3 weeks, 4 weeks, 1 month, 1.5 months, 2 months, 2.5months, 3 months or more. In some embodiments, the cells are divided andre-plated every 2 days, every 3 days, every 4 days, every 5 days, every6 days, every week or longer. In some embodiments, the culture mediacontaining the AR antagonist is refreshed every day, every 2 days, every3 days, every 4 days, every 5 days, every 6 days, every week or longer.In some embodiments, the AR antagonist is a second-generationantagonist. In some embodiments, the AR antagonist is ARN-509. In someembodiments, the AR antagonist is enzalutamide (MDV3100).

In some embodiments, the prostate cancer cell line is a human prostateadenocarcinoma cell line. In some embodiments, the prostate cancer cellline is an LNCaP cell line. In some embodiments, the prostate cancercell line overexpresses the androgen receptor. In some embodiments, theprostate cancer cell line is LNCaP/AR(cs) or LNCaP/AR(cs)-Luc.

Examples

These examples are provided for illustrative purposes only and not tolimit the scope of the claims provided herein.

Example 1: Generation of Drug Resistant Cell Line In Vivo

Cell lines resistant to treatment with the anti-AR compound ARN-509 weregenerated in vivo in mice bearing castration resistant human prostateadenocarcinoma (LNCaP/AR(cs)) xenograft tumors. The LNCaP/AR(cs) cellline over-expresses the androgen receptor (AR) 3-5 fold over theparental LNCaP cell line mimicking castration resistant prostate cancer(Chen et al. (2004) Nature Medicine 10:33-39).

LNCaP-AR(cs) xenograft tumors were grown in castrated six week old maleSCID Hairless Outbred mice (SHO, Charles Rivers Laboratories). 1×10⁶LNCaP-ARcs cells in 50% serum-free RPMI and 50% Matrigel™ weresubcutaneously injected (100 μl/animal) on the right flank of 10 mice3-5 days post castration. Tumor size was monitored daily. When tumorsreached an average volume of ˜200 mm³ (approximately 60 dayspost-injection), the animals began treatment with vehicle alone (n=1) or30 mg/kg ARN-509 (n=9) by QD dosing regimen (i.e. orally in 15% VitaminE-TPGS and 65% of a 0.5% w/v carboxymethyl cellulose (CMC) solution in20 mM citrate buffer (pH 4.0)). Initially, treatment with ARN-509induced tumor regression. Following approximately 75 days of dosing, asingle tumor resumed growth and progressed to a size greater than attreatment initiation. Once the resistant tumor reached ˜800 mm³, themouse was euthanized and the tumor was harvested. Tumor cells weremanually dispersed by homogenization with a 3 mL syringe. Tumor cellswere cultured in RPMI plus 10% FBS and 10 μM ARN-509. One resistant cellline was generated by this method.

Example 2: Generation of Drug Resistant Cell Lines In Vitro

Cell lines resistant to treatment with the anti-AR compounds ARN-509 andMDV3100 were generated in vitro using LNCaP human prostateadenocarcinoma cell lines.

LNCaP (ATCC), LNCaP/AR(cs) (Guo et al. (2006) Cancer Cell 0:309-19) andLNCaP/AR-Luc (Tran et al. Science (2009) 324(5928):787-90; Ellwood-Yenet al. (2006) Cancer Res. 66:10513-6) were maintained in RPMI 1640supplemented with 10% FBS (Hyclone). LNCaP (ATCC), LNCaP/AR(cs) orLNCaP/AR(cs)-Luc cells were cultured in increasing concentrations ofeither ARN-509 or MDV3100 over a course of 6 months. Initially, 50 mL ofcells were seeded into a 225 cm² cell culture flask at a concentrationof approximately 80,000 cells/mL and grown in RPMI plus 10% FBS in thepresence of 800 nM ARN-509 or MDV3100. Medium and drug were changedsemiweekly and the cells were passaged in 75 cm² cell culture flasks asneeded. The concentration of each compound was increased several timesfrom about 1.5 μM to about 6 μM as the growth rate of the drug-treatedcells increased to that of the untreated control cells. Afterapproximately 6 months of drug selection, the cells were maintained inRPMI plus 10% FBS and 6 μM ARN-509 or MDV3100. Following selection, 10independent ARN-509 and MDV3100 resistant cell lines were obtained. Twolines were derived from LNCaP (ATCC) cells selected in the presence ofARN-509. Four cell lines were derived from LNCaP/AR(cs), two followingtreatment with ARN-509 and two following treatment with MDV3100.LNCaP/AR(cs)-Luc cells were used to derive 4 resistant cell lines, twofrom ARN-509 treatment and two from MDV3100 treatment.

Example 3: Proliferation Assays to Test Drug Resistance

Cell proliferation assays were performed to test resistance of the celllines to ARN-509 and MDV3100 treatment.

Proliferation assays were performed on all ARN-509 and MDV3100 resistantcell lines by seeding 16 μL/well of cells at a density of 50,000 cellsper mL in phenol-red-free RPMI 1640 (with 5% CSS) into 384-well cellculture plate (Flat Clear Bottom Black Polystyrene TC-Treated 384 Wellplates (Corning)) and incubated for 2 days at 37° C. For agonist assays,11 point semi-log dilutions of each compound were made in culture mediumand 16 μL of each dilution was added to the cells. ARN-509, MDV3100 andbicalutamide were run at a final concentration ranging from 3.16×10⁻⁵ Mto 3.18×10⁻¹⁰ M, while the synthetic androgen methyltrienolone (R1881)was run at a final concentration range of 3.16×10⁻⁸ M to 3.18×10⁻¹³ M.For the antagonist mode assay, the compounds were diluted in culturemedium also containing 200 pM R1881 (PerkinElmer, Waltham, Mass.) (final[R1881]=100 pM) and then added to the cells (16 μL). After 7 days, 16 μLof CellTiter-Glo® Luminescent Cell Viability Assay (Promega, Madison,Wis.) was added directly to the cell cultures and Relative LuminescenceUnits (RLUs) measured according to the manufacturer's instructions.

In the agonist mode assay, percent viability of the samples wascalculated as: % viability=100×([RLU sample-RLU medium withoutcells]/[RLU 1881 treated cells-RLU medium without cells]) (Table 1A). Inthe antagonist mode assay, the percent viability of the samples wascalculated as: % viability=100×([RLU sample-RLU Day 0]/[RLU R1881treated cells−RLU Day 0]) (Table 1B).

TABLE 1A Agonist Proliferation Assay (% Viability) R1881 BicalutamideMDV3100 ARN-509 LNCaP 100.0 + + + LNCaP/AR(cs) 100.0 + + + Class 1 100.0++ ++ ++ Class 2 100.0 + ++ ++ ‘+’ = <30, ‘++’ = >30 [R1881] = 0.1 nM,[Antagonists] = 10 μM

TABLE 1B Antagonist Proliferation Assay (% Viability) R1881 BicalutamideMDV3100 ARN-509 LNCaP 100.0 + + + LNCaP/AR(cs) 100.0 + + + Class 1 100.0++ ++ ++ Class 2 100.0 ++ ++ ++ ‘+’ = <30, ‘++’ = >30 [R1881] = 0.1 nM,[Antagonists] = 10 μM

In the proliferation assays, both ARN-509 and enzalutamide were fullproliferative antagonists in all three LNCaP parental cell lines (Table1A, FIG. 1A). The resistant cell lines segregated into two distinctclasses. Unlike their parental cell lines, the first class of ARN-509-and MDV3100-resistant cells (Class 1) proliferate in the absence ofadded androgens. The ligand independent growth of the cells is unalteredin the presence of ARN-509, MDV3100 or bicalutamide. The syntheticandrogen, R1881, inhibits proliferation in the class 1 cells at highconcentrations. This growth inhibitory activity of R1881 is antagonizedby either MDV3100 or ARN-509, indicating that AR is still capable ofbinding MDV3100 and ARN-509 in these cell lines.

Class 1 resistant cell lines included the one cell line derived from theLNCaP-AR(cs) xenograft tumor, the 2 cell lines derived from LNCaP/AR(cs)cell selected in the presence of ARN-509, the 2 cell lines derived fromLNCaP/AR(cs) cells selected in the presence of MDV3100, the 2 cell linesderived from LNCaP/AR(cs)-Luc selected in the presence of ARN-509, andone of the cell lines derived from LNCaP/AR(cs)-Luc selected in thepresence of MDV3100.

The second class of MDV3100- and ARN-509-resistant cell lines (Class 2)remains androgen dependent for growth, similar to their parental celllines. However, unlike their activity on the parental cell lines,ARN-509 and MDV3100 can stimulate proliferation in the class 2 celllines. Bicalutamide, however, did not stimulate proliferation in theclass 2 cell lines. Class 2 resistant cell lines included the two celllines derived from LNCaP cells selected in the presence of ARN-509(LNCaP ARN-509r1 and LNCaP ARN-509r2) and one of the cell lines derivedfrom LNCaP/AR(cs)-Luc selected in the presence of MDV3100 (LNCaP ENZr2).

The partial agonist activity was independent of the compound utilizedfor selection; ARN-509 and enzalutamide displayed partial agonistactivity in all three cell lines regardless of the compound used toderive the resistance variants. Consistent with proliferative activity,ARN-509 or enzalutamide only partially antagonized androgen dependentgrowth of these resistant lines (Table 1B, FIG. 1B,C).

Example 4: Transcriptional Reporter Assays to Test Drug Resistance

Transcriptional reporter assays using an ARE response elementoperatively linked to a reporter gene were performed to test resistanceof the cells to ARN-509, MDV3100, and bicalutamide treatment.

Transcriptional reporter assays were performed on all resistant celllines by seeding 100 μL of cells at a density of 250,000 cells/mL into96-well cell culture plates in RPMI 1640 supplemented with 5% charcoalstripped serum and allowed to attach overnight at 37° C.

With the exception of the LNCaP/AR(cs)-Luc cells that contain anintegrated androgen responsive reporter, cells were transientlytransfected using Lipofectin® (Life Technologies) according to themanufacturer's protocol. For LNCaP and LNCaP/AR(cs) cells, triplicatetransfections were performed using 428 ng reporter vector (pGL4Pb-Luciferase (the rat probasin promoter in pGL4 (Promega, Madison,Wis.))), 50 ng pRL-CMV (normalization vector, Promega. Madison, Wis.)and 0.7 μL Lipofectin®. Following transfection, the cells were incubatedfor 4 hours.

Cells were then treated with the test compounds ARN-509, MDV3100 andbicalutamide. For agonist assays, the compounds were serially dilutedand 50 μL of compound plus RPMI 1640 plus 5% charcoal stripped FBS wasadded to the cells. For antagonist assays, the compounds were seriallydiluted and 50 μL of compound with RPMI plus 3 nM R1881 supplementedwith 5% charcoal stripped serum was added to the cells. Following 48hour incubation the medium was removed and the cells were lysed in 40 μLof lysis buffer (25 mM Tris Phosphate, 2 mM CDTA, 10% Glycerol, 0.5%Triton X-100, 2 mM DTT). Firefly luciferase activity was measuredimmediately following the addition of 40 μL luciferase buffer (20 mMtricine, 0.1 mM EDTA, 1.07 mM (MgCo₃)₄ Mg(OH)₂.5H₂O, 2.67 mM MgSO₄, 33.3mM DTT, 270 μM Coenzyme A, 470 μM luciferin, 530 μM ATP). Renillaluciferase was measured following the addition of 40 μL coelenterazinebuffer (1.1 M NaCl, 2.2 mM Na₂EDTA, 0.22 M K_(x)PO₄ (pH 5.1), 0.44 mg/mLBSA, 1.3 mM NaN₃. 1.43 μM coelenterazne, final pH adjusted to 5.0).

The two classes of ARN-509- and MDV3100-resistant cell lines identifiedin the proliferation assays also exhibited distinct properties in thetranscriptional assays. In transient transfection assays using the pGL4Pb-Luciferase reporters or in assays using the integratedprobasin-luciferase reporter (i.e. LNCaP/AR(cs)-Luc-derived cells),ARN-509 and MDV3100 were effective antagonists in theandrogen-independent class 1 resistant cells as evidenced by a decreasein luciferase activity relative to no treatment controls (Table 2).Bicalutamide, however, exhibited an increased agonist activity in class1 resistant cells compared to the parental cells. In class 2 resistantcells, MDV3100 was a weak partial agonist in the probasin-luciferasereporter assay, while bicalutamide and ARN-509 displayed no agonistactivity.

TABLE 2A Agonist Transcriptional Reporter Assay (% Max Activity) R1881Bicalutamide MDV3100 ARN-509 LNCaP >90 + + + LNCaP/AR(cs) >90 + + +Class 1 >90 ++ + + Class 2 >90 + ++ + ‘+’ = <5, ‘++’ = >5 [R1881] = 10nM, [Antagonists] = 50 μM

TABLE 2B Antagonist Transcriptional Reporter Assay (% Max Activity)R1881 Bicalutamide MDV3100 ARN-509 LNCaP >90 + + +LNCaP/AR(cs) >90 + + + Class 1 >90 ++ + ++ Class 2 >90 + ++ + ‘+’ = <5,‘++’ = >5 [R1881] = 10 nM, [Antagonists] = 50 μM

Example 5: Endogenous Gene Transcriptional Assays

The effects of R1881, MDV3100 and bicalutamide treatment on endogenousgene transcription was examined.

By Western blot, the AR levels in the class 1 resistant cell lines wereapproximately 2 to 4-fold higher than observed in the LNCaP/AR(cs) cellline (FIG. 2). Analogous to an approximate 3-fold increase in AR levelsbeing sufficient to support growth of LNCaP cells in a castrate settingin vivo, the further 2 to 4-fold elevation in AR levels may besufficient to promote proliferation in the absence of androgens invitro. In contrast, the AR levels of the class 2 resistant lines weresimilar to that observed in the parental cell lines. Thus, theconversion of enzalutamide and ARN-509 to partial agonists in the class2 cell lines was not due to AR overexpression. Minor differences intotal and phosphorylated Akt and Erk were observed with no consistentchanges seen in either class of resistant cell lines.

Total RNA was isolated using the Aurum™ total RNA isolation kit(BIO-RAD, Hercules, Calif.). RNA (1 μg) was reverse transcribed usingthe iScript cDNA synthesis kit (BIO-RAD, Hercules, Calif.) to producecDNA. Real-time PCR was performed using the Applied Biosystems 7900HTinstrument and SYBR Green PCR Master Mix (Applied Biosystems, FosterCity, Calif.). PCR reactions were performed in 6 μL according to themanufacturer's protocol and a thermocycle protocol of 95° C. for 10minutes followed by 40 cycles of 95° C. for 15 seconds and 58° C. for 1minute. Androgen responsive gene (PSA, SLUG, TMPRSS2, STEAP4, FKBP5,ORM1, NOV, FASN, NKX3.1, AMIGO2, BDNF, CAMK2N1, HPGD, NCAPD3, PLD1)expression was normalized to GAPDH expression and expressed relative tovehicle treatment of the parental cell line. Relative expression resultsare provided in Table 3A. Primers employed for PCR are listed in Table3B.

Similar compound and class selective agonist activities were observed onendogenous androgen-responsive genes, but in the context of theendogenous genes the transcriptional activity of MDV3100 is more evident(Table 3). In class 1 resistant cells, bicalutamide displays robusttranscriptional activity and MDV3100 is a weak transcriptional agonist.In contrast, in class 2 resistant cell lines, bicalutamide is a weaktranscriptional agonist while MDV3100 displays robust transcriptionalagonist activity on the genes tested.

TABLE 3A Endogenous Gene Transcriptional Activity (Fold Vehicle) PSASLUG TMPRSS2 STEAP4 FKBP5 ORM1 NOV LNCaP DMSO 1.0 1.0 1.0 1.0 1.0 1.01.0 R1881 ++ +++ ++ ++++ ++ +++ −− Bicalutamide + + + + + − +MDV3100 + + + − + + + LNCaP/AR(cs) DMSO 1.0 1.0 1.0 1.0 1.0 1.0 1.0R1881 +++ +++ ++ ++++ ++ ++++ −− Bicalutamide ++ + + ++ + +++ +MDV3100 + + + + + + + Class 1 DMSO 1.0 1.0 1.0 1.0 1.0 1.0 1.0 R1881 +++++ + ++++ +++ ++++ −− Bicalutamide + +++ + +++ ++ ++ +MDV3100 + + + + + + + Class 2 DMSO 1.0 1.0 1.0 1.0 1.0 1.0 1.0 R1881 ++++++ ++ ++++ +++ ++++ −− Bicalutamide + + + + + + + MDV3100 +++ +++ +++++ ++ +++ − [R1881] = 10 nM, [Antagonists] = 30 μM −− <0.1, − =0.1-1, + = 1-10, ++ = 10-50, +++ 50-500, ++++ >500

TABLE 3B Transcriptional Real-time PCR Oligonucleotide Sequence GeneForward Primer Sequence Reverse Primer Sequence AMIGO2AGAGACTCAGAGGCGACCAT ATCAGCAAACACAGCAGCTC (SEQ ID NO: 20)(SEQ ID NO: 21) BDNF AGAGCTGTTGGATGAGGACC AGAAAGGCTCCAAAGGCACTTGACTACT(SEQ ID NO: 22 (SEQ ID NO: 23) CAMK2N1 GACCAAGCGGGTTGTTATTGATGCCTTGTCGGTCATATTTTTCA (SEQ ID NO: 24) (SEQ ID NO: 25) FKBP5CGGAGAACCAAACGGA AAGGCTTCGCCCACAGTGAATGC (SEQ ID NO: 26) (SEQ ID NO: 27)HPGD ACAGCAGCCGGTTTATTGTGCTTC TGGCATTCAGTCTCACACCACTGT (SEQ ID NO: 28)(SEQ ID NO: 29) NCAPD3 ACCACTCACCATCATCTCA AGGCATGCTCTTCTTTGCCAGATCCTCGT(SEQ ID NO: 30) (SEQ ID NO: 31) NOV GCCTTACCCTTGCAGCTTACGAGCATGCTGTCCACTCTGT (SEQ ID NO: 32) (SEQ ID NO: 33) ORM1CTTGCGCATTCCCAAGTCAGATGT TTTCCTCTCCTTCTCGTGCTGCTT (SEQ ID NO: 34)(SEQ ID NO: 35 PLD1 GAGCCTGCTACAGATGGTCA TGTCTACCAGCAGGACGAAG(SEQ ID NO: 36) (SEQ ID NO: 37) PSA CCTCCTGAAGAATCGATTCCGAGGTCCACACACTGAAGTT (SEQ ID NO: 38) (SEQ ID NO: 39) SLUGTTTCTGGGCTGGCCAAACATAAGC ACACAAGGTAATGTGTGGGTCCGA (SEQ ID NO: 40)(SEQ ID NO: 41) STEAP4 CGGCAGGTGTTTGTGTGTGGAAAT AGAAGACACACAGCACAGCAGACA(SEQ ID NO: 42) (SEQ ID NO: 43) TMPRSS2 TAGTGAAACCAGTGTGTCTGCCCAAGCGTTCAGCACTTCTGAGGTCTT (SEQ ID NO: 44) (SEQ ID NO: 45) FASNCGCTCTGGTTCATCTGCTCTG TCATCAAAGGTGCTCTCGTCTG (SEQ ID NO: 46)(SEQ ID NO: 47) NKX3.1 TGGAGAGGAAGTTCAGCCATCAGA AGGAGAGCTGCTTTCGCTTAGTCT(SEQ ID NO: 48) (SEQ ID NO: 49)

In a separate experiment, gene expression of the following genes wereanalyzed in LNCaP, LNCaP/AR(cs), LNCaP/AR-Luc. LNCaP ARN-509r1, LNCaPARN-509r2 and LNCaP/AR-Luc ENZr2 cells: PLD, CAM2KN, NOV, BDNF, AMIGO2,FASN, TMPRSS2, NKX3.1, PSA, FKBP5, HPGD, NCAPD3, SLUG, STEAP4, and ORM.Cells were cultured for 3 days in hormone depleted medium followed bytreatment with vehicle, 1 nM R1881 or 30 μM compound. Gene expressionwas normalized to GAPDH as described above. Results are presented inTables 4A and 4B.

TABLE 4A LNCaP. LNCaP/AR(cs) and resistant line transcription LNCaPLNCaP/AR(cs) LNCaP ARN-509r1 ARN- ARN- ARN- Gene Vehicle 509 ENZ R1881Vehicle 509 ENZ R1881 Vehicle 509 ENZ R1881 AMIGO2 1.00 1.12 1.20 0.681.00 0.72 1.13 0.54 1.00 0.62 0.99 0.21 BDNF 1.00 1.09 0.85 0.40 1.000.85 1.13 0.48 1.00 0.90 1.58 0.31 CAM2KN1 1.00 1.17 1.39 0.13 1.00 0.801.11 0.05 1.00 0.37 0.59 0.01 FASN 1.00 1.34 1.24 5.58 1.00 0.75 1.197.11 1.00 1.04 1.53 3.12 FKBP5 1.00 0.99 1.04 54.95 1.00 0.99 1.71 97.011.00 2.58 9.45 53.45 HPGD 1.00 1.48 1.78 100.43 1.00 1.18 2.01 183.551.00 2.36 10.20 61.39 NCAPD3 1.00 1.16 1.20 104.69 1.00 0.91 1.22 93.051.00 1.29 3.12 90.51 NKX3.1 1.00 0.90 1.66 30.06 1.00 1.13 2.51 8.821.00 6.54 11.55 8.11 NOV 1.00 1.73 2.57 0.15 1.00 1.04 1.27 0.04 1.001.40 1.39 0.03 ORM1 1.00 0.71 1.13 873.10 1.00 0.84 3.58 3444.31 1.0015.89 205.07 1296.13 PLD1 1.00 1.09 0.70 0.02 1.00 1.04 0.65 0.02 1.000.33 0.24 0.03 PSA 1.00 0.66 1.69 47.84 1.00 1.43 2.69 19.16 1.00 32.6757.68 85.63 SLUG 1.00 1.27 2.35 129.79 1.00 1.03 2.06 89.88 1.00 4.6642.52 164.28 STEAP4 1.00 0.78 1.54 639.15 1.00 0.90 1.95 1314.23 1.003.03 32.22 1184.45 TMPRSS2 1.00 0.77 1.68 22.16 1.00 1.06 2.36 17.511.00 10.20 23.75 37.27 LNCaP LNCaP ARN-509r2 Gene Vehicle ARN-509 ENZR1881 Vehicle ARN-509 ENZ R1881 AMIGO2 1.00 1.12 1.20 0.68 1.00 0.670.63 0.55 BDNF 1.00 1.09 0.85 0.40 1.00 1.04 0.77 0.47 CAM2KN1 1.00 1.171.39 0.13 1.00 0.46 0.38 0.02 FASN 1.00 1.34 1.24 5.58 1.00 0.98 0.934.82 FKBP5 1.00 0.99 1.04 54.95 1.00 8.00 3.41 48.50 HPGD 1.00 1.48 1.78100.43 1.00 1.49 4.56 59.30 NCAPD3 1.00 1.16 1.20 104.69 1.00 1.13 1.3554.95 NKX3.1 1.00 0.90 1.66 30.06 1.00 3.73 6.28 10.20 NOV 1.00 1.732.57 0.15 1.00 1.39 0.71 0.07 ORM1 1.00 0.71 1.13 873.10 1.00 3.94 23.75625.99 PLD1 1.00 1.09 0.70 0.02 1.00 0.81 0.29 0.02 PSA 1.00 0.66 1.6947.84 1.00 1.91 2.48 7.89 SLUG 1.00 1.27 2.35 129.79 1.00 1.31 9.5877.17 STEAP4 1.00 0.78 1.54 639.15 1.00 1.45 4.69 377.41 TMPRSS2 1.000.77 1.68 22.16 1.00 3.07 4.86 15.14

TABLE 4B LNCaP/AR-Luc and LNCaP/AR-Luc ENZr2 transcription LNCaP/AR-LucLNCaP/AR-Luc ENZr2 Gene Vehicle ARN-509 ENZ R1881 Vehicle ARN-509 ENZR1881 AMIGO2 1.00 1.13 1.44 0.54 1.00 0.99 0.78 0.49 BDNF 1.00 1.17 1.080.18 1.00 0.56 0.44 0.12 CAM2KN1 1.00 1.13 1.51 0.11 1.00 0.65 0.57 0.11FASN 1.00 1.08 1.40 3.48 1.00 1.72 1.20 4.44 FKBP5 1.00 1.16 1.46 20.821.00 2.46 3.03 23.43 HPGD 1.00 1.88 2.51 2.41 1.00 1.22 1.61 1.39 NCAPD31.00 1.09 1.33 17.27 1.00 1.38 1.39 31.12 NKX3.1 1.00 1.14 1.68 11.241.00 4.82 5.21 10.13 NOV 1.00 2.55 1.95 0.47 1.00 1.21 1.20 0.27 ORM11.00 1.27 1.39 7.89 1.00 15.24 17.88 347.29 PLD1 1.00 1.45 1.33 0.151.00 0.46 0.74 0.21 PSA 1.00 0.60 0.44 2.10 1.00 4.59 3.48 16.91 SLUG1.00 1.13 2.73 48.84 1.00 5.98 12.30 160.90 STEAP4 1.00 0.88 1.23 20.251.00 1.66 4.38 79.89 TMPRSS2 1.00 0.74 1.35 3.46 1.00 4.44 4.23 7.73

Example 6: Assays for Mechanisms of Resistance

Array CGH, mRNA expression profiling and sequence analysis of patientderived prostate cancer tumors as well as many animal and in vitromodels have implicated multiple pathways in the progression to thecastration resistant state. Three of the most commonly activatedpathways indentified in castration resistant prostate cancer are thePI3K, Raf and AR pathways. In this example, Akt and Erk phosphorylationwas evaluated by Western blot to assess the activation states of thePI3K and Raf pathway respectively.

To evaluate the mode of drug resistance in the class 1 and class 2 celllines, Western analysis was performed to assess AR protein levels andthe activation state of several cellular signaling pathways known tomodulate AR activity and commonly activated in castration resistantprostate cancer. Relative expression of AR, Akt, phosphorylated Akt(Ser473), p44/42 MAPK (Erk1/2), phosphorylated p44/42 MAPK (Erk1/2)(Thr202/Tyr204), tubulin and actin were determined.

For Western analysis, cells were grown in RPMI 1640 supplemented with 5%charcoal stripped serum for 3 days. Cells were lysed in modifiedradioimmunoprecipitation buffer (mRIPA; 10 mM Tris, 150 mM NaCl, 1%(v/v) NP-40, 0.5% deoxycholate, 0.1% SDS, 5 mM EDTA, pH 7.4) containingHalt™ Protease and Phosphatase Inhibitor Cocktail (Thermo Scientific).Total protein of the clarified lysates was quantitated by Lowry Assay(Biorad DC protein assay). NuPAGE® LDS Sample Buffer and Sample ReducingAgent were added to the lysates and heated to 70° C. for 10 minutes. 20μg of total cell protein was separated on a NuPAGE 4-12% Bis TrisAcrylamide Gel and transferred to a nitrocellulose membrane using anXcell II™ blot module (Invitrogen). Membranes were incubated in BlockingBuffer (LI-COR, Lincoln, Nebr.) for 30 minutes at room temperature,followed by 60 minute incubations with primary antibodies againstAndrogen Receptor (Santa Cruz Biotechnology cat. No. SC-816). Akt andPhospho-Akt (Ser473) (Cell Signaling cat. Nos. 9272 and 4058respectively), p44/42 MAPK (Erk1/2) and Phospho-p44/42 MAPK (Erk1/2)(Thr202/Tyr204) (Cell Signaling cat. Nos. 4695 and 4376s respectively)and tubulin or actin (Sigma cat. No T6199 and A4700 respectively).Following incubation with an IRDye® Conjugated Goat Anti Mouse or RabbitIgG (LI-COR), protein bands were quantified using an Odyssey® InfraredImaging System.

By Western blot, the AR levels in the class 1 resistant cell lines wereapproximately 2 to 4-fold higher than observed in the LNCaP/AR(cs) cellline (FIG. 2). Analogous to an approximate 3-fold increase in AR levelsbeing sufficient to support growth of LNCaP cells in a castrate settingin vivo, the further 2 to 4-fold elevation in AR levels may besufficient to promote proliferation in the absence of androgens invitro. In contrast, the AR levels of the class 2 resistant lines weresimilar to that observed in the parental cell lines. Thus, theconversion of enzalutamide and ARN-509 to partial agonists in the class2 cell lines was not due to AR overexpression. Minor differences intotal and phosphorylated Akt and Erk were observed with no consistentchanges seen in either class of resistant cell lines.

Example 7: Determination of Mutant AR Sequence

MDV3100 and ARN-509 are transcriptional and proliferative agonists inthe class 2 resistant cell lines, while bicalutamide remains anantagonist. AR expression in class 2 resistant cells was similar to theparental cell line (Example 6). Thus, the sequence of AR in class 2resistant cells was determined to ascertain whether a mutation of the ARligand binding domain promotes the gain of function activity.

cDNA generated by reverse transcription of RNA isolated from class 1 andclass 2 cells (see Example 5) was used as a template to sequence AR.Using a series of oligonucleotides, overlapping segments encompassingthe AR ligand binding domain (c. 2013-2757) were generated by PCR usingPhusion® polymerase (New England Biolabs) using the manufacturer'sprotocol. The PCR products were gel purified to remove non-specificbands as well as unincorporated oligonucleotides. The purified PCRproducts were sequenced using internal oligonucleotides.

A single nucleic acid mutation was identified within the AR ligandbinding domain at nucleotide position 2626 in three independentlyderived cell lines. The missense mutation identified in all lines wasThymine (T) to Cytosine (C) that converts Phenylalanine (F) at aminoacid position 876 of the encoded polypeptide to Leucine (L) (SEQ ID NO:19). Additionally, sequencing of individual subcloned PCR products fromthe LNCaP/AR-Luc ENZr2 cell line indicated that in all cell lines theF876L mutation arose in the endogenous AR allele.

F876 lies in helix 11 in a region of AR ligand binding pocket that is ahotspot for CRPC AR mutations (FIG. 1D). However, unlike T877 and L701,which coordinate hydrogen bonding to the 17α-OH group ofdihydrotestosterone, F876 contributes to a small hydrophobic core formedby residues in helix 11 (F786, L880), the loop between helices 11 and 12(F891) and helix 3 (F697. L701). While similar residues and hydrophobicligand interactions are conserved in the estrogen and progesteronereceptor, F876 has not been implicated in high affinity binding orsteroid selectivity. Consistent with the relatively minor role F876 ispredicted to play in steroid binding, the AR-F876L mutation has not beenreported in prostate cancer or androgen insensitive populations.

Example 8: Expression of the Mutant AR in AR-Deficient Cells

To confirm that the F876L mutation confers agonist activities to ARN-509and MDV3100, the point mutation was generated in the context of thefull-length wild-type AR and the LNCaP T877A mutant receptor. The F876Land F876L/T877A mutants were generated in the plasmid pcDNA3-AR usingthe QuickChange II Site-Directed Mutagenesis Kit (Agilent Technologies,Santa Clara, Calif.) according to the manufacturer's protocol.

Transcriptional reporter assays using an ARE response elementoperatively linked to a reporter gene were performed to test thetranscriptional activity of the mutant AR in response to ARN-509,MDV3100 and bicalutamide treatment.

Transcriptional reporter assays were performed by seeding 100 μL ofHEPG2 cells at a density of 250,000 cells/mL into 96-well cell cultureplates in MEM supplemented with 10% charcoal stripped serum and allowedto attach overnight at 37° C.

Cells were transiently transfected using Lipofectin® (Life Technologies)according to the manufacturer's protocol. Triplicate transfections wereperformed using 378 ng reporter vector (4X ARE-Luciferase or pGL4Pb-Luciferase (the rat probasin promoter in pGL4 (Promega, Madison,Wis.)), 50 ng pcDNA-AR (wild-type or mutant) 50 ng pRL-CMV(normalization vector) and 0.7 μL Lipofectin®. Following transfection,the cells were incubated for 4 hours.

Following the incubation, the cells were treated with the test compoundsARN-509, MDV3100 and bicalutamide. For agonist assays, the compoundswere diluted 1:6 and 50 μL of compound in MEM plus 5% charcoal strippedFBS was added to the cells for a final concentration range of 30 μM to0.64 nM. For antagonist assays, the compounds were serially diluted with1 nM R1881 (for wild-type AR) or 5 nM R1881 (for F876L AR).

Following 48 hour incubation the medium was removed and the cells werelysed in 40 μL of lysis buffer (25 mM Tris Phosphate, 2 mM CDTA, 10%Glycerol, 0.5% Triton X-100, 2 mM DTT). Firefly luciferase activity wasmeasured immediately following the addition of 40 μL luciferase buffer(20 mM tricine, 0.1 mM EDTA, 1.07 mM (MgCo₃)₄ Mg(OH)₂.5H₂O, 2.67 mMMgSO₄, 33.3 mM DTT, 270 μM Coenzyme A, 470 μM luciferin, 530 μM ATP).Renilla luciferase was measured following the addition of 40 μLcoelenterazine buffer (1.1 M NaCl, 2.2 mM Na₂EDTA, 0.22 M K_(x)PO₄ (pH5.1), 0.44 mg/mL BSA, 1.3 mM NaN₃, 1.43 μM coelenterazine, final pHadjusted to 5.0).

In transient transfection assays, second-generation AR antagonistsARN-509 and MDV3100 induced AR dependent transcriptional activity in thecontext of the F876L or F876L/T877A mutant AR, while induction frombicalutamide was minimal (Table 5). For example, in HepG2 cells usingeither a 4XARE-luciferase or Pb-luciferase reporter, ARN-509 andMDV3100, but not bicalutamide, induced AR dependent transcriptionalactivity in the context of the F876L or F876L/T877A mutant AR. Thisindicates that mechanism of resistance in the class 2 cell lines is theAR F876L mutation.

TABLE 5 AR Transcriptional Activity (Fold DMSO) MDV3100 R1881Bicalutamide (enzalutamide) ARN509 AR WT +++ + + + AR F876L +++ + ++++ + = <20, ++ = 10-200, +++ > 200 [R1881] = 100 nM, [Antagonists] = 6.3μM

A second experiment was performed 4X-ARE-Luciferease report to confirmthe above results. In this experiment, first generation anti-androgensnilutamide and hydroxyflutamide were also compared along withbicalutamide, ARN-509 and enzalutamide. The AR transcriptional reporterassays were performed essentially as described above with minormodifications. Triplicate transfections were performed using 50 ngpCDNA3-AR or pCDNA3-AR mutant, 65 ng 4X ARE-Luciferase, 20 ng pRL(Promega), and 25 ng pCMX. For agonist assays, compounds were seriallydiluted, and 50 μL of compound plus RPMI 1640 supplemented with charcoalstripped serum was added to the cells. For antagonist assays, thecompounds were serially diluted, and 50 μL of compound with RPMIsupplemented with charcoal stripped serum plus methyltrienolone (R1881)were added to the cells. The final R1881 concentration used in theantagonist assays was 1 nM with the exception of F876L for which 5 nMR1881 was used.

As shown in FIGS. 4A-B, in the context of wild-type AR. ARN-509 andenzalutamide were full antagonists and with minimal agonist activity in4X-ARE androgen responsive transcriptional reporter assays. However, incells expressing AR-F876L or AR F876L/T877A, enzalutamide and ARN-509were partial transcriptional agonists (FIG. 4A). Conversely, the firstgeneration anti-androgens bicalutamide, nilutamide and hydroxyflutamidedisplayed minimal agonist activity on the F876L mutant (Table 6, FIG.4B) (Emax=percent maximal R1881 response). Enzalutamide and ARN-509 werefull antagonists on AR mutants T877A, L701H, H874Y and W741C that eitherconfer resistance to first generation AR antagonists or broadensteroidal ligand specificities in CRPC patients.

TABLE 6 4X ARE Reporter Assay WT IC₅₀ WT F876L IC₅₀ F876L Compound (□M)Emax (□M) Emax ARN-509 0.79 ± 0.15 1.3 ± 0.3 0.09 ± 0.06 49.7 ± 11.1Enzalut- 1.12 ± 0.17 0.4 ± 0.1 0.13 ± 0.04 20.2 ± 5.2  amideBicalutamide 1.65 ± 0.93 10.0 ± 2.9  3.63 ± 0.04 0.7 ± 0.3 Hydroxy- 0.36± 0.04 28.9 ± 5.0  2.60 ± 6.61 0.8 ± 0.2 flutamide Nilutamide 1.11 ±0.17 5.1 ± 2.1 7.59 ± 1.18 0.6 ± 0.1

To test DNA binding competency of the F876L mutants VP16-AR fusionconstructs were generated. pVP16-AR was generated by subloningfull-length human AR into pVP16 (Clontech). AR point mutations weregenerated in VP16-AR using the QuickChange II Site-Directed MutagenesisKit (Agilent Technologies, Santa Clara, Calif.) according to themanufacturer's protocol.

Transcription assays were performed essentially as described above.Triplicate transfections were performed using 35 ng pVP16-AR orpVP16-F876L, 70 ng 4X ARE-Luciferase, 20 ng pRL (Promega), and 35 ngpCMX. 4X ARE-luciferase reporter activity was monitored in the presenceof increasing compound concentrations in the absence or presence of 90pM R1881 (for wild-type VP16-AR) or 1 nM R1881 (for F876L VP16-AR).Luciferase activity was measured as described above.

Reflective of the transcriptional reporter assay, in the wild-typeVP16-AR assay, which monitors the DNA binding competency of thereceptor, enzalutamide and ARN-509 were full antagonists (Table 7, FIG.4A) (Emax=percent maximal R1881 response). However, in the context ofthe VP16-AR-F876L, ARN-509 and enzalutamide stimulated AR DNA binding.Thus, the mutation of AR F876 to L was sufficient to convert the 2ndgeneration anti-androgens, enzalutamide and ARN-509, to partialagonists.

TABLE 7 AR-VP16 WT IC₅₀ WT F876L IC₅₀ F876L Compound (□M) Emax (□M) EmaxARN-509 0.16 ± 0.06  3.98 ± 0.27 0.03 ± 0.02 53.98 ± 1.45  Enzalut- 0.21± 0.07  2.65 ± 0.73 0.05 ± 0.01 34.32 ± 5.38  amide Bicalutamide 0.18 ±0.10 32.77 ± 5.76 2.51 ± 1.11 2.20 ± 1.35 Hydroxy- 0.03 ± 0.01 42.28 ±4.44 0.97 ± 0.27 5.36 ± 5.35 flutamide Nilutamide 0.13 ± 0.08 33.53 ±9.75 2.12 ± 0.68 2.90 ± 1.80

Example 9: Stable Cell Line Generation

In this example, cell lines were generated with stable expression of ARF876L mutant. pSRαF876L, pQCXIN-AR and pQCXIN-F876L retroviruses werefirst generated by co-transfecting GP2-293 cells with pVSV-G (Clontech)according to the manufacturer's protocol.

PC3 cells stably expressing wild-type or AR-F876L were generated bytransducing PC3 cells with either pQXIN-AR or pQXIN-F876L retrovirus andselection in RPMI 1640 medium containing 500 μg/mL gentamycin.

LNCaP cells stably expressing AR-F876L were generated by eithertransfecting LNCaP cells with pCDNA-F876L or transducing LNCaP cellswith SRαF876L retrovirus. Individual clones of LNCaP/pCDNA-F876L wereisolated following selection in 400 μg/mL gentamycin. LNCaP/SRαF876Lcell pools were selected 400 mg/mL gentamycin.

AR protein expression of all cell lines was validated by westernanalysis using AR N-20 antibody (Santa Cruz Biotechnology).

Example 10: Equilibrium AR Binding Assays

Competitive binding assays of wild-type AR vs. F876L AR were performedas described in Clegg et al. (2012) Cancer Research 72:1494-503 usingPC3 cells stably expressing wild-type human AR or AR-F876L as describedabove. Ki was calculated as Ki=IC50/(1+([³H-R1881]/Kd)), [³H-R1881]=0.6nM.

In equilibrium AR binding assays, ARN-509 and enzalutamide bound themutant with 30 and 48-fold higher affinity, respectively (Table 8, FIGS.5A-B) (Kd for R1881: AR=0.5 nM; AR-F877L=0.64 nM). Thus, increasedagonist activity on AR is associated with increased binding affinity toboth wild-type and F876L receptor, suggesting that the agonistconfirmation enables higher affinity through decreased dissociationconstant.

TABLE 8 AR binding, WT K_(i) AR binding, F876L K_(i) Compound (nM) (nM)ARN-509 18.07 ± 7.46 0.68 ± 0.15 Enzalut-  26.30 ± 12.77 0.60 ± 0.17amide Bicalutamide  26.56 ± 12.51 360.36 ± 283.85 Hydroxy- 14.56 ± 8.25150.57 ± 55.10  flutamide Nilutamide 17.74 ± 5.65 197.42 ± 9.26 

Example 11: Expression of AR Target Genes in and Proliferation of F876LStable Prostate Cancer Cell Lines

As shown above, expression of AR-F876L was sufficient to conferenzalutamide and ARN-509 resistance in transient reporter based assays.In this example, the effects of F876L on endogenous AR target genes andproliferation in prostate cancer cells stably expressing the mutant wasexamined. Two LNCaP cell lines (LNCaP/SRαF876L and LNCaP/pCDNAF876L)were engineered as described in Example 9 to overexpress AR-F876L atlevels comparable to the LNCaP/AR(cs) model.

To measure AR levels in the cells, protein extracts were generated fromLNCaP, LNCap/AR(cs), LNCaP/SRαF876L and LNCaP/pCDNAF876L cells culturedin hormone depleted medium for 3 days. AR protein levels were analyzedby western blot. AR levels were quantified and normalized to actin andexpressed relative to AR expression in LNCaP cells (FIG. 6)

For endogenous target gene analysis, LNCaP/AR(cs). LNCaP SRαF876L, andLNCaP/pCDNAF876L cells were cultured for 3 days in hormone depletedmedium followed by treatment with vehicle, 1 nM R1881 or 1, 3, 10 and 30μM ARN-509 or enzalutamide in the presence or absence on 1 nM R1881.

For the proliferation assays, LNCaP/AR(cs), LNCaP SRαF876L, andLNCaP/pCDNAF876L cells were cultured in the presence of hormone depletedmedium for 2 days followed by ligand treatment for 7 days as describedabove. For antagonist assays, ARN-509 or enzalutamide were added in thepresence of 200 pM R1881 (100 pM final concentration). Proliferation wasquantified by CellTiter-Glo luminescence based viability assay asdescribed above.

In LNCaP/AR(cs) cells, ARN-509 and enzalutamide had little effect on theinduction of AR target genes or proliferative activity (FIG. 7A, Table9A). Both antagonists blocked R1881 induced transcription andproliferation to levels consistent with their agonist activity at thehighest concentration (FIG. 7B, Table 9B). In contrast, in F876L-ARexpressing cells, both enzalutamide and ARN-509 demonstrated robusttranscriptional and proliferative agonist activity (FIGS. 7A and 7B,Tables 9C-F).

TABLE 9A LNCaP/AR(cs) Agonist Transcription −R1881 1 nM EnzalutamideARN-509 Gene Vehicle R1881 0.3 μM 1 μM 3 μM 10 μM 30 μM 0.3 μM 1 μM 3 μM10 μM 30 μM AMIGO2 1.00 0.98 0.68 0.61 0.62 0.66 1.22 1.14 0.69 0.890.65 2.41 BDNF 1.00 0.86 1.04 0.92 0.88 0.95 0.98 1.15 0.93 1.03 1.031.80 CAM2KN1 1.00 0.04 0.80 0.70 0.71 0.64 0.64 0.90 0.76 0.99 0.78 1.56FASN 1.00 4.12 0.47 0.32 0.29 0.31 0.58 0.46 0.40 0.42 0.41 1.30 FKBP51.00 100.51 0.91 0.62 0.75 0.61 0.85 0.99 0.71 0.91 0.75 1.87 HPGD 1.00324.60 0.74 0.57 0.61 0.63 1.29 0.81 0.56 0.78 0.61 1.86 NCAPD3 1.0095.54 0.66 0.57 0.47 0.56 0.79 0.72 0.74 0.73 0.74 1.34 NKX3.1 1.0012.72 0.71 0.52 0.51 0.86 1.63 1.11 0.68 0.73 0.85 2.24 NOV 1.00 0.051.12 0.91 0.80 1.02 1.01 1.12 1.00 1.11 0.98 2.07 ORM1 1.00 6987.01 0.920.90 1.06 0.71 2.02 1.37 1.79 1.20 0.97 1.35 PLD1 1.00 0.03 0.77 0.620.63 0.56 0.56 1.28 0.66 0.88 0.65 1.33 PSA 1.00 22.14 0.42 0.32 0.380.74 1.60 0.44 0.49 0.58 0.61 1.13 SLUG 1.00 91.84 0.53 0.55 0.31 0.510.91 0.38 0.42 0.52 0.56 1.36 STEAP4 1.00 1498.46 0.75 0.73 0.52 1.161.28 0.94 0.77 1.05 0.56 1.01 TMPRSS2 1.00 35.42 0.75 0.53 0.63 0.891.45 0.99 0.64 1.04 0.62 2.78

TABLE 9B LNCaP/AR(cs) Antagonist Transcription +1 nM R1881 1 nMEnzalutamide ARN-509 Gene Vehicle R1881 0.3 μM 1 μM 3 μM 10 μM 30 μM 0.3μM 1 μM 3 μM 10 μM 30 μM AMIGO2 1.00 0.98 0.49 0.19 0.48 0.78 0.92 0.300.31 0.52 0.60 0.76 BDNF 1.00 0.86 0.61 0.28 0.63 0.99 1.12 0.43 0.350.67 0.74 0.88 CAM2KN1 1.00 0.04 0.04 0.06 0.27 0.50 0.56 0.04 0.06 0.190.43 0.42 FASN 1.00 4.12 1.30 0.42 0.71 0.46 0.59 1.92 1.52 1.08 0.600.64 FKBP5 1.00 100.51 23.51 5.64 3.32 1.41 1.50 33.14 22.49 12.56 2.741.08 HPGD 1.00 324.60 99.16 16.30 13.19 3.85 4.25 105.97 76.25 32.198.36 2.78 NCAPD3 1.00 95.54 23.74 4.35 3.14 1.29 1.27 43.93 32.00 15.572.39 0.96 NKX3.1 1.00 12.72 7.70 3.77 6.72 4.70 5.03 8.32 9.92 12.017.22 5.49 NOV 1.00 0.05 0.11 0.14 0.61 1.00 0.92 0.03 0.09 0.31 0.860.82 ORM1 1.00 6987.01 3521.95 503.02 257.85 43.91 22.70 5100.90 2679.731031.40 156.90 16.42 PLD1 1.00 0.03 0.02 0.02 0.13 0.42 0.54 0.02 0.020.04 0.11 0.32 PSA 1.00 22.14 22.76 8.82 11.75 6.59 5.65 19.09 21.7523.57 12.90 7.20 SLUG 1.00 91.84 50.08 10.20 10.56 5.26 5.22 71.33 62.0050.70 11.15 5.49 STEAP4 1.00 1498.46 585.81 109.37 74.44 13.61 7.791019.98 742.61 256.89 32.98 6.86 TMPRSS2 1.00 35.42 19.88 7.72 10.513.58 4.62 19.07 24.11 23.38 11.45 5.94

TABLE 9C LNCaP/SRαF876L Agonist Transcription −R1881 1 nM EnzalutamideARN-509 Gene Vehicle R1881 0.3 μM 1 μM 3 μM 10 μM 30 μM 0.3 μM 1 μM 3 μM10 μM 30 μM AMIGO2 1.00 0.29 0.58 0.32 0.47 0.40 0.31 0.27 0.47 0.230.34 0.27 BDNF 1.00 1.65 1.04 1.30 1.01 0.99 1.55 0.79 1.07 0.75 0.840.94 CAM2KN1 1.00 0.03 0.52 0.48 0.38 0.23 0.37 0.30 0.24 0.17 0.21 0.18FASN 1.00 3.76 0.50 0.64 0.58 1.09 1.34 0.64 1.01 0.93 1.50 2.77 FKBP51.00 66.89 1.38 1.14 2.54 9.61 23.67 2.66 5.95 5.56 13.02 27.89 HPGD1.00 182.19 0.68 0.96 2.79 18.98 55.76 4.18 7.90 10.12 25.79 69.22NCAPD3 1.00 31.69 0.77 1.01 1.09 3.56 8.83 1.39 1.58 1.69 3.53 9.35NKX3.1 1.00 10.80 4.26 5.54 7.05 11.94 14.20 7.12 9.47 7.96 9.85 12.67NOV 1.00 0.06 0.55 0.28 0.55 0.42 0.21 0.27 0.51 0.31 0.29 0.17 ORM11.00 6535.38 2.17 4.85 18.77 242.08 2114.41 44.44 58.96 101.45 459.301357.12 PLD1 1.00 0.02 0.67 0.76 0.60 0.42 0.41 0.49 0.44 0.30 0.45 0.36PSA 1.00 3.43 1.95 2.25 3.02 4.05 5.02 3.71 3.26 3.00 5.07 5.16 SLUG1.00 99.20 1.21 1.55 3.28 16.87 107.64 5.56 5.91 8.15 26.35 56.48 STEAP41.00 1706.02 1.13 2.15 9.98 96.53 343.81 20.36 27.49 46.06 187.24 479.64TMPRSS2 1.00 25.55 3.11 3.85 5.39 9.20 18.61 6.36 6.29 5.84 10.90 14.20

TABLE 9D LNCaP/SRαF876L Antagonist Transcription +1 nM R1881 1 nMEnzalutamide ARN-509 Gene Vehicle R1881 0.3 μM 1 μM 3 μM 10 μM 30 μM 0.3μM 1 μM 3 μM 10 μM 30 μM AMIGO2 1.00 0.29 0.23 0.29 0.33 0.39 0.40 0.170.22 0.14 0.18 0.18 BDNF 1.00 1.65 0.53 0.64 0.62 0.51 0.71 0.74 0.760.57 0.50 0.63 CAM2KN1 1.00 0.03 0.08 0.12 0.19 0.24 0.32 0.03 0.03 0.060.11 0.17 FASN 1.00 3.76 1.29 1.22 0.85 0.94 1.58 2.23 2.03 1.39 1.302.66 FKBP5 1.00 66.89 17.90 14.89 10.21 17.33 40.52 36.57 39.48 26.4629.94 22.71 HPGD 1.00 182.19 49.66 30.03 21.62 34.77 93.52 149.34 134.7079.93 70.80 131.79 NCAPD3 1.00 31.69 6.34 4.28 2.21 3.44 13.64 19.8315.47 8.71 6.50 11.82 NKX3.1 1.00 10.80 21.66 20.78 16.19 11.84 15.2612.63 14.12 11.34 10.15 13.64 NOV 1.00 0.06 0.12 0.28 0.25 0.33 0.260.05 0.06 0.09 0.11 0.09 ORM1 1.00 6535.38 386.40 216.67 137.73 661.513496.87 3335.14 2343.29 1469.18 1608.16 3440.86 PLD1 1.00 0.02 0.04 0.080.14 0.37 0.48 0.01 0.01 0.02 0.08 0.20 PSA 1.00 3.43 5.84 5.63 4.474.54 4.64 4.93 4.38 4.59 5.28 4.17 SLUG 1.00 99.20 85.97 64.63 35.5048.80 161.58 85.97 64.63 35.50 48.80 161.58 STEAP4 1.00 1706.02 259.94147.25 83.20 275.88 645.04 259.94 147.25 83.20 275.88 645.04 TMPRSS21.00 25.55 14.05 13.81 11.78 12.92 20.19 14.05 13.81 11.78 12.92 20.19

TABLE 9E LNCaP/pCDNAF876L Agonist Transcription −R1881 1 nM EnzalutamideARN-509 Gene Vehicle R1881 0.3 μM 1 μM 3 μM 10 μM 30 μM 0.3 μM 1 μM 3 μM10 μM 30 μM AMIGO2 1.00 0.92 1.28 0.82 0.87 0.72 0.91 1.07 0.86 1.250.60 1.55 BDNF 1.00 1.01 1.54 1.04 1.11 0.82 0.64 1.01 0.76 0.87 0.851.16 CAM2KN1 1.00 0.02 0.55 0.96 0.51 0.37 0.23 0.47 0.55 0.34 0.41 0.27FASN 1.00 22.20 0.91 0.72 0.48 1.27 3.66 1.16 1.42 1.59 1.79 7.86 FKBP51.00 145.63 2.18 2.91 4.28 10.54 42.25 7.24 7.82 9.52 17.39 55.55 HPGD1.00 854.42 4.70 6.32 13.26 26.78 105.81 15.36 19.27 29.25 47.33 173.82NCAPD3 1.00 169.67 1.95 1.94 3.68 9.41 35.36 5.83 6.52 8.28 20.42 51.1.3NKX3.1 1.00 9.67 3.76 3.71 3.57 4.69 8.12 6.07 5.72 5.93 7.05 11.69 NOV1.00 0.08 1.73 1.62 2.19 0.88 0.49 1.24 1.01 0.82 0.86 0.72 ORM1 1.0012816.69 116.91 195.36 659.73 2530.13 4760.77 932.41 1371.33 2307.293322.63 5541.08 PLD1 1.00 0.75 1.37 0.80 0.69 0.29 0.45 0.78 0.69 1.010.68 0.48 PSA 1.00 12.17 3.56 4.04 5.29 9.53 11.70 6.74 7.19 8.25 10.0612.99 SLUG 1.00 268.77 1.99 3.53 4.74 14.91 55.93 7.84 8.70 10.91 21.2171.08 STEAP4 1.00 3084.81 10.38 15.58 46.50 240.68 520.15 113.39 113.29173.77 317.80 597.09 TMPRSS2 1.00 26.85 4.98 6.46 6.09 8.51 21.78 9.498.51 9.70 11.09 23.01

TABLE 9F LNCaP/pCDNAF876L Antagonist Transcription +1 nM R1881 1 nMEnzalutamide ARN-509 Gene Vehicle R1881 0.3 μM 1 μM 3 μM 10 μM 30 μM 0.3μM 1 μM 3 μM 10 μM 30 μM AMIGO2 1.00 0.92 0.51 0.43 0.39 0.49 0.52 0.240.31 0.43 0.41 0.40 BDNF 1.00 1.01 0.59 0.71 0.53 0.50 0.41 0.28 0.410.42 0.45 0.34 CAM2KN1 1.00 0.02 0.05 0.16 0.17 0.21 0.14 0.01 0.02 0.060.11 0.06 FASN 1.00 22.20 5.29 2.44 1.55 2.08 4.22 3.89 5.52 3.22 2.103.98 FKBP5 1.00 145.63 53.18 26.29 10.03 14.22 32.97 45.69 48.95 38.8924.82 30.26 HPGD 1.00 854.42 149.44 59.67 21.66 35.90 96.55 192.05170.69 107.79 73.28 87.03 NCAPD3 1.00 169.67 101.65 31.49 14.34 16.6942.06 68.41 90.52 62.27 22.96 44.10 NKX3.1 1.00 9.67 8.53 7.05 5.69 5.547.61 3.08 5.95 5.42 4.81 5.24 NOV 1.00 0.08 0.08 0.17 0.32 0.49 0.390.02 0.10 0.12 0.26 0.18 ORM1 1.00 12816.69 4375.20 1581.76 587.001377.92 3765.54 4802.10 4943.10 3366.19 2576.38 2470.99 PLD1 1.00 0.750.08 0.12 0.09 0.11 0.12 0.04 0.12 0.05 0.06 0.04 PSA 1.00 12.17 16.0812.73 7.92 8.12 14.27 10.36 14.01 12.21 10.27 13.14 SLUG 1.00 268.77166.04 86.01 30.23 36.56 98.34 112.06 134.56 113.34 69.55 85.38 STEAP41.00 3084.81 524.97 156.24 47.11 92.80 214.69 633.57 587.91 376.66195.78 232.63 TMPRSS2 1.00 26.85 19.03 16.05 8.14 8.92 15.32 12.13 15.7514.19 12.99 12.67

Example 12: Interaction of N and C Expression of AR Target Genes in andProliferation of F876L Stable Prostate Cancer Cell Lines

Interaction of the AR amino-terminus with the AR carboxy-terminus isimportant for the full AR transactivation capacity. Many AR full andpartial agonists stimulate the AF2 dependent N-C interaction. A N-C twohybrid interaction assay was performed to assess the interaction of theAR N- and C-termini in the F87L mutant in the presence of ARN-509 andenzalutamide.

pM-AR1-660, pVP16-AR507-919 and pVP16-F876L507-919 were generated bysubcloning appropriate PCR products from pCDNA3-AR and pCDNA3-F876L intopM and pVP16 (Clontech). For N-C terminal interaction assays, triplicatetransfections were performed using 50 ng pM-AR1-660, 75 ngpVP16-AR507-919 or pVP16-F876L507-919, 25 ng pMH100-Luc and 10 ng pRL(Promega). Transfected cells were incubated 4 hours then treated withligand. ARN-509 and enzalutamide were assayed at 8 μM and R1881 at 1 nM.

Consistent with their transcriptional activities, enzalutamide andARN-509 promoted the N-C interaction of AR-F876L but not wild-type AR(FIG. 8). Thus, the agonist activity of ARN-509 and enzalutamide onAF-F876L is associated with an agonist-like AF-2 conformation.

Example 13: Chromatin Immunoprecipitation Assay of AR

Transcriptional activation of androgen regulated AR target genesrequires agonist-induced DNA binding and subsequent recruitment oftranscriptional coregulators. To confirm the VP16-AR reporter resultsindicating ARN-509 and enzalutamide stimulate AR-F876L DNA binding, weperformed chromatin immunoprecipitation (ChIP) analysis of 6 AR targetgenes from cells treated with R1881 and/or each antagonist wasperformed.

ChIP assays were performed as described in Joseph et al. (2009) PNAS USA106:12178-83]. Briefly, LNCaP/AR(cs) and LNCaP SRαF876L cells wereplated in 150 mm dishes (7×10⁶ cells in 20 mL) in RPMI 1640 supplementedwith 10% CSS for 3 days. Cells were treated with 10 μM antagonist in thepresence or absence of 1 nM R1881 for 4 hours. Following ligandtreatment, formaldehyde was added to the media to a final concentrationof 1%, incubated for 10 min and quenched with glycine (125 mM finalconcentration) for 5 minutes. Cells were washed 3× with PBS containing1× Halt™ Protease & Phosphatase Single-Use Inhibitor Cocktail (1× PI,Thermo Scientific), pelleted, lysed in 1 mL RIPA buffer (50 mM TrispH7.5, 0.15 M NaCl, 1% NP-40, 0.5% Na-deoxycholate, 0.05% SDS, 1 mMEDTA, 1× PI) and sonicated until the average DNA size fragment was ≈500bp. The sonicated cross-linked chromatin was diluted into 3.3 mL RIPAand precleared with 100 mL 50% protein A/G agarose slurry (SC-2003,Santa Cruz Biotechnology) containing 200 mg per mL sonicated salmonsperm DNA and 500 mg per mL of BSA. One mL of precleared chromatin wasthen immunoprecipitated with 15 μg anti-AR (SC-816, Santa CruzBiotechnology) or normal rabbit IgG (SC-2027, Santa Cruz Biotechnology),for 2 hours at 4° C. and 100 mL of a 50% slurry of protein A/G agarosebeads were added and incubated overnight at 4° C. Beads were washed 2times sequentially in low-salt buffer (50 mM HEPES pH 7.8, 140 mM NaCl.1 mM EDTA, 1% Triton X-100. 0.1% Na-deoxycholate, 0.1% SDS), high-saltbuffer (same as low-salt with 500 mM NaCl), LiCl buffer (20 mM Tris pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), and TEbuffer (50 mM Tris pH 8.0, 1 mM EDTA). All washing steps were performedin the presence of 1× PI. Protein-DNA complexes were eluted in 225 mLElution buffer (50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS) at 65° C. twicefor 15 minutes. Eluted protein-DNA complexes were reverse cross-linkedin the presence of NaCl overnight at 65° C. and further treated withEDTA and proteinase K at 42° C. for 1 hour. The DNA fragments werepurified in 10 mM Tris pH 8.5 using the QIAquick PCR purification kit(Qiagen), diluted and analyzed by real-time PCR using iTaq SYBR GreenSupermix with ROX (Bio-Rad). The samples were amplified on the ABI7900HT instrument. Oligonucleotide primer sequences are listed in Table8.

TABLE 8 ChIP Real-time PCR Oligonucleotide Sequence GeneForward Primer Sequence Reverse Primer Sequence PSA E2ACCTGCTCAGCCTTTGTCTCTGAT AGATCCAGGCTTGCTTACTGTCCT (SEQ ID NO: 50)(SEQ ID NO: 51) PSA D1 ATTCTGGGTTGGGAGTGCAAGGA AGGAGACATGCCCAGGATGAAAC AA (SEQ ID NO: 52) (SEQ ID NO: 53) STEAP4 ACTAGGCAGGACATTGACATCCCACAGTAAACCTCTCCACACATGG A C (SEQ ID NO: 54) (SEQ ID NO: 55) FASNTATGACACCCAGGGCTTTCGTTC TAACGTTCCCTGCGCGTTTACAGA A (SEQ ID NO: 57)(SEQ ID NO: 56) TMPRSS2 TCCCAAATCCTGACCCCA ACCACACAGCCCCTAGGAGA(SEQ ID NO: 58) (SEQ ID NO: 59) NKX3. 1 ACAGGGTGGCCCAAATAGAACCCTGTCTTGGACAAGCGGAGA (SEQ ID NO: 60) (SEQ ID NO: 61) ORM1GGGTCATTTCCACCACCTCAAAC GGAGAAAGGCCTTACAGTAGTCT A C (SEQ ID NO: 62)(SEQ ID NO: 63)

In the LNCaP/AR(cs) cells, R1881 promoted AR DNA (FIG. 9). Consistentwith the VP16-AR reporter data, both ARN-509 and enzalutamide promotedAR DNA binding LNCaP/SRαF876L cells. In the presence of R1881, allantagonists inhibited R1881-stimulated AR DNA binding to levelsconsistent with their partial agonist or antagonist activity in bothcell lines (FIG. 9).

Example 14: In Vivo Effects of AR F876L

To determine whether the F876L alteration conveys resistance toenzalutamide and ARN-509 in vivo, LNCaP cell lines stably expressingF876L AR were injected (s.c.) into castrated immune-deficient mice andtumors established.

All animal studies were carried out under protocols approved by theInstitutional Animal Care and Use Committees and institutionalguidelines for the proper, humane use of animals in research werefollowed. In vivo xenograft experiments were carried out in SCIDHairless Outbred (SHO) male mice (Charles River Laboratories). Mice wereorchiectomized under isoflorane anesthesia and were given 7-10 days torecover. LNCaP/AR(cs) or LNCaP/SRαF876L cells (as described above) weresuspended in 50% RPMI, 50% Matrigel (BD Biosciences), and 3×10⁶cells/xenograft were injected in a volume of 100 μL. Animals wereobserved weekly until tumor growth was apparent. After 40-60 dayspost-injection, animals were randomized into cohorts of equivalent tumorburden mean (150-250 mm³) and range. All compounds were administereddaily by oral gavage at a dose of 30 mg/kg/day compound. For allLNCaP/AR(cs) xenograft studies ARN-509 and enzalutamide drug stocks wereprepared in 18% PEG-400, 1% Tween-80 and 1% povidone, and wereformulated for dosing in 15% Vitamin E-TPGS and 65% of a 0.5% w/v CMCsolution in 20 mM citrate buffer (pH 4.0). ARN-509 and enzalutamidepharmacokinetics were assessed at the end of study as describedpreviously (Clegg et al. (2012) Cancer Research 72:1494-503).

Consistent with the in vitro data, neither ARN-509 nor enzalutamide 30mg/kg/day impacted the growth of LNCaP/AR/SRαF876L tumors (FIG. 10).This lack of activity was not a function of unexpectedly low compoundexposure as day 28 plasma drug levels were quantified and wereconsistent with previous LNCaP/AR xenograft studies (Table 9). Inaddition, in a parallel experiment, ARN-509 30 mg/kg/day exhibitedrobust anti-tumor activity in the LNCaP/AR(cs) model, consistent withprevious results (FIG. 10).

TABLE 9 LNCaP/SRαF876L Xenograft Pharmacokinetics AUC₀₋₂₄ C₂₄ T_(1/2)(μg · hr/ C_(max) T_(max) Compound Dose (μg/mL) (hr) mL) (μg/mL) (hr)Enzalutamide 30 mg/kg 9.14 9.9 527.3 33.5 1.0 ARN-509 30 mg/kg 1.02 7.198.9 9.11 1.0

Example 15: An Open-Label. Phase ½ Safety. Pharmacokinetic, andProof-of-Concept Study of ARN-509 in Patients with Progressive AdvancedCastration-Resistant Prostate Cancer (CRPC)

In this study, DNA was isolated from 29 patient plasma samples patientsparticipating in a Phase ½ clinical study ARN-509 treatment for prostatecancer. These were analyzed using the emulsion PCR-based BEAMingTechnology method (Dressman et al. (2003) PNAS USA 100:8817-22). BEAMinghas been successfully used to detect a variety of tumor derivedmutations in driver oncogenes such as PIKC3a and K-ras in ctDNA derivedfrom human plasma (Diehl et al. (2008) Nature Medicine 14:985-90). TheAR F876L mutation was identified in 3 of the 29 patient samples tested.

The clinical study performed was multi-institution, first in man. Phase½, dose-escalation and proof-of-concept study across 9 dose levels inwhich eligible patients with progressive advanced CRPC received oraldoses of ARN-509 on an outpatient basis to determine the safety,pharmacokinetics (PK) and preliminary evidence of the anti-tumor effectsof ARN-509.

Patients with mCRPC were assigned sequentially to dose levels in cohortsof 3 to 6 patients per dose level using standard 3×3 dose-escalationcriteria.

The objective was to determine the maximum tolerated dose (MTD) and/orrecommended Phase 2 dose (RP2D) of ARN-509 that leads to a dose-limitingtoxicity (DLT) in a maximum of 30% of patients. A DLT is generallydefined as any Grade 1 or higher seizure, any Grade 3-4 non-hematologictoxicity (GI toxicities must persist at Grade 3-4 despite maximalmedical therapy) and/or grade 4 hematologic toxicity of more than 5 daysduration, defined by CTCAE V4.0, and that is assessed as related toARN-509 treatment. A schematic of the study design is provided in FIG.11.

Eligible patients who signed informed consent documents were initiallyenrolled into a dose escalation cohort where they will receive a singleoral dose of ARN-509 followed by a one-week observation period (PKWeek). Continuous dosing began on Cycle 1 Day 1 assuming no unacceptabletoxicities were observed.

A minimum of 3 subjects at each dose level were monitored for a DLTthrough day 28 of Cycle 1. If no DLTs were observed in the first 3patients at each dose level, subsequent enrollment proceeded at the nextdose level. If 2 or more patients experienced a DLT at a given doselevel or a single episode of seizure of any grade was observed at agiven dose level, dose escalation was stopped and the MTD was defined asthe previous dose level. If no DLTs were observed, RP2D was based on theoverall pharmacokinetic and safety profile of ARN-509 and the optimalbiological dose determined from preclinical data, and not necessarilythe MTD.

The starting dose was 30 mg/day, with escalations to 60 mg, 90 mg, 120mg, 180 mg, 240 mg, 300 mg, 390 mg, and 480 mg daily. It was anticipatedthat these dose levels span the anticipated pharmacologically activedose range and be within the safety margin indicated by the preclinicaltoxicology results.

Following the selection of 240 mg as the RP2D, additional eligiblepatients were enrolled in the Phase 2 portion of the study, consistingof 3 concurrent expansion cohorts at the MTD and/or RP2D to gatheradditional safety information and provide an initial signal ofanti-tumor activity. The three expansion cohorts included:

1. Non-metastatic CRPC treatment naïve (50 patients with non-metastaticCRPC who are chemotherapy and abiraterone treatment naïve);

2. Metastatic CRPC treatment-naïve (20 patients with mCRPC who arechemotherapy and abiraterone naïve); and

3. Metastatic CRPC abiraterone treated (10-20 patients).

It was expected that each patient with mCRPC would receive at least 3cycles (12 weeks) of continuous treatment and each patient withnon-metastatic CRPC will receive at least 4 cycles (16 weeks) ofcontinuous treatment. Treatment was discontinued at any time forprotocol-defined disease progression or unacceptable toxicity. Tumorevaluations were performed every 3 cycles (12 weeks) for patients withmCRPC and every 4 cycles (16 weeks) for patients with non-metastaticCRPC. Safety was assessed from the first dose through at least fourweeks after the last dose or until resolution of drug-related toxicity,or when toxicity is deemed irreversible, whichever was longer. Theeffect of food on the absorption of ARN-509 and the effect of ARN-509 onventricular repolarization was evaluated in the Phase 2 expansion phaseat selected clinical sites.

Analysis of the samples using BEAMing technology in the current ARN-509clinical study was carried out by Inostics GMBH. Blood was collected inK2-EDTA evacuated tubes and mix thoroughly by slowly inverting severaltimes. Within 30 minutes of collection tubes were spun at 2000×g for 15minutes. Plasma was decanted, transferred to cryo storage tubes. Within90 minutes of decantation, plasma was stored at −70° C. or lower untilanalysis. DNA was purified from 300-500 μl plasma aliquots and extractedas described in Diehl et al. (2008) Nature medicine 14:985-90. Mutationdetection was performed according to BEAMing technology as described inDiehl et al. Briefly, in the initial PCR step, the target region (˜100bp) was amplified using gene-specific primers with tag sequences andsubjected to an emulsion PCR containing primer coated magnetic beads.After emulsion PCR discrimination of wildtype and mutant beads wasperformed by allele-specific hybridization followed flow cytometry. Flowcytometry results were analyzed using FCS Express (De Novo Software, LosAngeles, Calif.) resulting in the quantification of the ratio of themutant allele over the wild type alleles.

Samples were analyzed for the presence of wild type AR or 3 single pointmutant alleles that could result in F876L (t2988c, c2990a, and c2990g(or t2626c, c2628a, and c2928g, respectively, relative to the AR nucleicacid coding sequence set forth in SEQ ID NO: 18). Analyzed mutations andthe technical sensitivity of the BEAMing Method are shown in Table 10.For detection, the frequency has to be above the total amount of genomeequivalent used per assay. For example, if in a sample, 1,000 genomicequivalent are present, yet the calculated fraction of mutant DNAmolecules is 0.02% (1 mutant allele in 5,000 wild-type alleles), thesamples is scored as wild type.

TABLE 10 AR nucleotide changes monitored by BEAMing assay NucleotideNucleotide Amino Acid Amino Acid Position Change Position Change c.2626t > c 876 F > L c.2628 c > a 876 F > L c.2628 c > g 876 F > L

Results

A subset of patients across all dose groups exhibited PSA response with14/30 patients exhibiting a 12 week≧50% decline in PSA compared tobaseline. The PSA response for the 29 patients screened is depicted inFIG. 12A. Pre-treatment and during treatment plasma samples wereanalyzed. Time of BEAMing analysis is indicated by the terminal end ofthe PSA response line. Eighteen out of the 29 patients had PSA above ofbaseline at time of analysis indicating either intrinsic or acquiredresistance to ARN-509.

Three probes were designed to monitor the 3 nucleotide changes that canencode for the F876L amino acid substitution. Dilution mixingexperiments with the mutant sequence and wild-type DNA indicated atechnical sensitivity of 0.02% (potential to detect 1 mutant sequenceamong 5000 wild-type). In an initial screen of plasma samples of 29ARN-509 treated patients, evidence of the mutation was detected in 3patients (Tables 11 and 12). At time of BEAMing analysis, Patient 7 and10 had PSA levels above baseline, whereas Patient 13 has evidence ofrising PSA above the treatment nadir (FIG. 13). In all 3 patients, thenucleotide change c2628a was detected. In one of these 3 patients(Patient 10) the t2626c mutant was also detected, indicative ofpolyclonal disease. F876L encoding mutations were not detected in any ofpre-treatment samples (0/29) suggesting that if present prior to ARN-509treatment they were below the limit of detection or that the mutationsarose de novo during ARN-509 treatment. In either scenario, the datasupport the hypothesis that the selective outgrowth of lesions bearingthe mutant allele to levels sufficient to detect in ctDNA is dependenton chronic exposure to ARN-509 and is associated with rising PSA. Tofurther establish the association of F876L with progressive disease, weanalyzed plasma samples taken at additional timepoints from the 3patients scored positive during the initial screen (Table 12) In patient10, the mutation was not detected at the one other timepoint analyzed(Cycle 4; PSA 102% of TO). In Patient 13, the mutation was not detectedat Cycle 4 (PSA 16.2% of baseline) or at Cycle 12 (patient was scoredpositive at Cycle 11). The mutant sequence at Cycle 11 was at the limitof detection and is estimated to arise via amplification of a singlemutant molecule. Although PSA of Patient 13 was slowly rising from thetreatment nadir at Cycle 11 and 12, at both time points PSA wasstill>60% below study start, and thus frank resistance had not yetemerged. Identification of the mutant sequence at the limit of detectionlikely reflects presence of a relatively rare, mutant clone that haspotential to expand under continued selective pressure and eventuallydrive progressive disease.

Given the relatively long duration of treatment of Patient 7, plasmafrom additional time points during evident PSA reduction; (>90% declinefrom baseline; Cycle 4, 8 and 10) and at initial PSA rise from its nadir(Cycle 15 and 19) (FIG. 13) was analyzed. Interestingly, mutations werenot detected in the 3 samples from treatment cycle 4, 8 and 10 whereasthe c2628a mutation was detected in the 2 samples analyzed from initialPSA rise (Cycle 15 and 19). These clinical data are consistent with thepreclinical data indicating that the F876L amino acid change issufficient to convey resistance to ARN-509.

TABLE 11 BEAMing Results from F876L Positive Patients PSA MutantFrequency Treatment [Percent Genotypic [mutant/w.t. beads × 100] PatientCycle* of Day 0] Call c2990a c2990g t2988c 7 0 100 Wild-type — — — 7 41.4 Wild-type — — — 7 8 3.3 Wild-type — — — 7 10 5.6 Wild-type — — — 715 41.2 Mutant 0.162 — — 7 19 97.2 Mutant 5.005 — — 7 22 281.0 Mutant1.002 — — 10 0 100 Wild-type — — — 10 4 102 Wild-type — — — 10 7 245Mutant 0.051 — 0.12 13 0 100 Wild-type — — — 13 4 16.2 Wild-type — — —13 11 31.7 Mutant 0.065 — — 13 12 39.5 Wild-type — — — *Treatment cyclewas 4 weeks; Cycle 0 is pre-treatment timepoint.

TABLE 12 Primary F876L BEAMing of ARN-509-001 Patients PSA at TimeBEAMing of BEAMing During 12 week Analysis Analysis Baseline TreatmentPSA Treatment [Percent of Genotypic Genotypic Patient Response Cycle*Baseline] Call^(#) Call 1 30.49 19 195.4 w.t. w.t. 2 −61.8 10 337.08w.t. w.t. 3 22.7 4 122 w.t. w.t. 4 12.4 5 134 w.t. w.t. 5 −70.65 8 16w.t. w.t. 6 −90.02 10 84.6 w.t. w.t. 7 −98.6 22 281 w.t. Mutant 8 −62.216 10.2 w.t. w.t. 9 26.38 7 185 w.t. w.t. 10 2.33 7 245 w.t. Mutant 11−49.76 8 143.88 w.t. w.t. 12 −56.65 7 99.47 w.t. w.t. 13 −83.79 11 31.7w.t. Mutant 14 −43.21 11 150.5 w.t. w.t. 15 164.14 3 220 w.t. w.t. 1689.09 4 189 w.t. w.t. 17 −45.86 4 54.14 w.t. w.t. 18 −95.65 6 7.34 w.t.w.t. 19 −71.19 11 196.86 w.t. w.t. 20 −30.88 21 89.3 w.t. w.t. 21 −74.4310 46.91 w.t. w.t. 22 −82.7 25 0.19 w.t. w.t. 23 97.78 8 222.46 w.t.w.t. 24 −74.86 25 4.89 w.t. w.t. 25 −30.07 12 161 w.t. w.t. 26 96.51 5214.85 w.t. w.t. 27 −0.89 13 20.69 w.t. w.t. 28 −33.59 10 126 w.t. w.t.29 −58.44 13 105 w.t. w.t.

Example 16: Method for Generation of Cell Lines for Drug Screening

To identify compounds that retain AR antagonist activity in the contextof the F876L mutation of the androgen receptor, a number of in vitro andin vivo assays as described above are adapted.

In an in vitro setting, a transient transfection transcription assayssimilar to that described in Example 8 is used to identify compoundsthat are devoid of agonist activity and fully antagonize both thewild-type as well as F876L mutant AR transcriptional activity. HEPG2cells or any eukaryotic cell in which AR transcriptional activity can bemonitored is employed for this screen.

As an alternative to transient transfection, the transcriptionalreporter and F876L AR is stably integrated in a number of cell lines andused for screening compounds. The stable integration of the mutant F876LAR into an androgen sensitive prostate cancer cell line such as LNCaP,LaPC4 or VCaP through the use of plasmid (i.e. pCDNA3.1) or viral basedintegration allows the screening and evaluation of compounds intranscriptional, proliferation and xenograft setting. Briefly, the F876LAR is cloned into a retroviral expression vector such as pQCXIP(Clontech, Mountain View, Calif.). The resultant plasmid is then used togenerate high titer viral stocks for use in the generation of stablytransduced cell lines according to the manufacturer's protocol. Theresulting cell lines are used in transient transfection transcriptionalassays as described in Example 4, endogenous gene transcriptional assaysas described in Example 5, proliferation assays as described in Example3 or xenograft studies as described in Example 1.

Alternatively the cells are further modified by the stable integrationof an AR responsive reporter such as Cignal Lenti AR Reporter (Qiagen,Valencia. Calif.) allowing reporter based compound screening without theneed for transient transfection.

The examples and embodiments described herein are for illustrativepurposes only and various modifications or changes suggested to personsskilled in the art are to be included within the spirit and purview ofthis application and scope of the appended claims.

What is claimed is:
 1. A method for determining whether a subject is orwill become less responsive to therapy with a first- orsecond-generation androgen receptor (AR) antagonist, comprising: (a)testing a sample containing a nucleic acid molecule encoding an ARpolypeptide from the subject to determine whether the encoded ARpolypeptide is modified at an amino acid position corresponding to aminoacid position 876 of the amino acid sequence set forth in SEQ ID NO: 1;and (b) characterizing the subject as resistant or will become resistantto therapy with a first- or second-generation AR antagonist if thesubject has the modification.
 2. A method for optimizing the therapy ofa subject receiving a first- or second-generation AR antagonist fortreatment of a cancer, comprising: (a) testing a sample containing anucleic acid molecule encoding an AR polypeptide from the subject todetermine whether the encoded AR polypeptide is modified at an aminoacid position corresponding to amino acid position 876 of the amino acidsequence set forth in SEQ ID NO: 1; and (b) if the subject has themodification, discontinuing treatment with the first- orsecond-generation AR antagonist or; and (c) if the subject does not havethe modification, then (i) continuing treatment with a first- orsecond-generation AR antagonist; or (ii) administering athird-generation AR antagonist that inhibits the modified receptor; or(iii) both discontinuing treatment with a first- or second-generation ARantagonist and administering a third-generation AR antagonist thatinhibits the modified receptor.
 3. A method for screening compounds thatantagonize a modified AR, comprising: (a) expressing a modified AR in acell, wherein the modified AR is modified at an amino acid positioncorresponding to amino acid position 876 of the amino acid sequence setforth in SEQ ID NO: 1; (b) contacting the cell with a test compoundbeing screened; and (c) detecting the level of AR activity in the cellby analyzing the expression of the reporter gene, the cell comprisingthe reporter gene operably linked to an androgen responsive promoter. 4.The method of claim 3, wherein the test compound (a) exhibits fullantagonist activity toward the modified AR receptor; (b) does notexhibit agonist activity toward the modified AR receptor; or (c) bothexhibits full antagonist activity toward the modified AR receptor anddoes not exhibit agonist activity toward the modified AR receptor. 5.The method of claim 3, wherein the modification is a substitution ordeletion of the amino acid at position 876 of the AR polypeptide.
 6. Themethod of claim 5, wherein the modification is a substitution ofphenylalanine at position 876 of the AR polypeptide, the phenylalaninebeing replaced by leucine, isoleucine, valine, alanine, glycine,methionine, serine, threonine, cysteine, tryptophan, lysine, arginine,histidine, proline, tyrosine, asparagine, glutamine, aspartic acid, orglutamic acid.
 7. The method of claim 6, wherein the phenylalanine atposition 876 of the AR polypeptide is replaced by glycine, alanine,valine, leucine, or isoleucine.
 8. The method of claim 7, wherein thephenylalanine at position 876 of the AR polypeptide is replaced byleucine.
 9. The method of claim 3, wherein the cell is deficient for theexpression of wild-type AR, expresses a low level of wild-type AR, orexpresses a modified AR receptor.
 10. The method of claim 3, wherein thecell is a HeLa, CV1, COS7, HepG2, HEK-293, DU145, PC3, TSY-PR1, LNCaP,CWR, VCaP or LAPC4 cell.
 11. The method of claim 3, wherein the promotercomprises an androgen response element.
 12. The method of claim 11,wherein the androgen response element is 4X ARE or a probasin element.13. The method of claim 3, wherein the promoter is a probasin, aprostate specific antigen, MMTV LTR, FASN, STEAP4, TMPRSS2, ORM1, orNKX3.1 promoter.
 14. The method of claim 3, wherein the reporter geneencodes a protein that is a luciferase, a fluorescent protein, abioluminescent protein, or an enzyme.
 15. A method of treating cancercomprising administering to a subject in need of such treatment atherapeutically effective amount of a third-generation AR antagonistidentified by the method of claim
 3. 16. The method of claim 15, whereinthe cancer is a prostate cancer, a breast cancer, a bladder cancer or ahepatocellular cancer.
 17. The method of claim 16, wherein the cancer isa castration resistant prostate cancer.
 18. The method of claim 15,wherein the subject expresses a mutant AR, wherein the mutant ARcomprises a substitution or a deletion of the amino acid at amino acidposition 876 in the AR polypeptide.
 19. The method of claim 18, whereinthe mutant AR comprises a substitution at amino acid position 876 in theAR polypeptide and the substitution is F876L.
 20. The method of claim15, wherein the third-generation AR antagonist is administered with anadditional therapeutic agent.
 21. The method of claim 20, wherein thethird-generation AR antagonist and the additional therapeutic agent areadministered sequentially, simultaneously or intermittently.
 22. Themethod of claim 20, wherein the additional therapeutic agent is ahormone, hormone receptor agonist or antagonist, corticosteroid,anti-emetic agent, analgesic, anti-cancer agent, anti-inflammatoryagent, kinase inhibitor, HSP90 inhibitor, or histone deacetylase (HDAC)inhibitor.
 23. The method of claim 20, wherein the additionaltherapeutic agent is a gonadotropin-releasing hormone (GnRH) agonist orantagonist.
 24. The method of claim 23, wherein the GnRH agonist isleuprolide, bruserelin or goserelin.
 25. A method of maintenance therapyin a patient having a cancer, comprising: (a) administering to thepatient a maintenance therapy regimen comprising administering atherapeutically effective dose of first- or second-generation ARantagonist; and (b) monitoring the patient at predetermined intervals oftime over the course of the maintenance therapy regimen to determinewhether the subject has mutation in an endogenous gene encoding AR thatresults in a modification at an amino acid position corresponding toamino acid position 876 of the amino acid sequence set forth in SEQ IDNO:
 1. 26. The method of claim 25, wherein monitoring comprises: testinga sample containing a nucleic acid molecule encoding a AR polypeptidefrom the subject to determine whether the encoded AR polypeptide ismodified at an amino acid position corresponding to amino acid position876 of the amino acid sequence set forth in SEQ ID NO:
 1. 27. The methodof claim 25, wherein the method further comprises discontinuingmaintenance therapy regimen if the subject has the mutation orcontinuing maintenance therapy regimen if the subject does not have themodification.
 28. The method of claim 25, wherein the method furthercomprises administering third-generation AR antagonist that inhibits themodified AR if the subject has the modification.
 29. The method of claim25, wherein the modification in the AR polypeptide is F876L.
 30. Themethod of claim 25, wherein the first- or second-generation ARantagonist inhibits a wild-type AR polypeptide by competitiveantagonism.
 31. The method of claim 25, wherein the second-generation ARantagonist is selected from among ARN-509, enzalutamide (MDV3100), andRD162.
 32. The method of claim 25, wherein the cancer is a prostatecancer, a breast cancer, a bladder cancer, or a hepatocellular cancer.33. The method of claim 32, wherein the cancer is prostate cancer. 34.The method any claim 33, wherein the cancer is a castration resistantprostate cancer.
 35. The method claim 25, wherein the predeterminedinterval of time is every week, every month, every 2 months, every 3months, every 4 months, every 5 months, every 6 months, every 7 months,every 8 months, every 9 months, every 10 months, every 11 months, orevery year.